Fig S1 Functional categorization of differentially

Unidentified (50%) Aging (0.85%) Anatomical structure development (2.24%) Anatomical structure maturation (0.85%) Developmental maturation (1.06%) Fruit ripening (0.85%) Multicellular organismal development (2.24%) Multicellular organismal process (2.34%) Photosynthesis, Light Harvesting (1.49%) Photosynthesis, Light reaction (1.6%) Photosynthesis (3.2%) Protein-Chromophore linkage (1.06%) Single organism developmental process (2.24%) Single-multicellular organism (2.34%) System development (2.02%)

Unidentified (64.03%) Choloroplast part (1.92%) Choloroplast Thylakoid membrane (1.28%) Choloroplast Thylakoid (1.38%) Choloroplast (3.09%) external encapsulating structure (1.6%) extracellular region (2.66%) organelle subcompartment (1.38%) Photosynthetic membrane (2.34%) photosystem I reaction centre (0.42%) photosystem I (1.49%) photosystem II (1.7%) photosystem (2.24%) Plastid part (1.92%) Plastid Thylakoid membrane (1.28%) Plastid Thylakoid (1.38%) Plastid (3.09%) Thylakoid membrane (1.81%) Thylakoid part (2.34%) Thylakoid (2.56%)

Unidentified (76.84%) Chlorophyll binding (1.17%) hydrolase activity, acting on glycosyl bond (3.09%) hydrolase activity, hydrolysing O-glycosyl compound (3.09%) hydrolase activity (9.39%)

Fig S1. S1 Functional categorization of differentially expressed genes in rin mutant (wild type BR Vs rin BR+3) based on Gene Ontology (GO) biological process (A), cellular component (B) and molecular function (C).

A

B

5 4.5

2.5

4

Wild type rin mutant

3.5

Wild type rin mutant

2

3 1.5

2.5 2

1

1.5 1

0.5

0.5 0

0 MG

BR

BR+3

BR+7

MG

BR

BR+3

BR+7

Fig S2. APX and CAT activities in wild type and rin mutant fruits. (A) APX activity decreased gradually during ripening of wild type tomato fruits. However, significant increase in APX activity was detected in rin mutant, as compare to wild type, at the ripening stages. (B) CAT activity was found to be variable during ripening of the wild type and rin mutant fruits. Increased CAT activity was recorded in rin fruits at BR+3 stage.

Table S1 List of differentially expressed genes in rin mutant. Serial No.

ID

Length (bp)

1

Les.1.1.S1_at

499

Functional annotation to tomato genome database [ITAG release 2.3 predicted proteins (SL2.40); www.solgenomics.net]

Bits Score

E-Value

236

1E-20

*******

*******

422

4E-42

414

1E-41

402

7E-40

506

7E-52

606

1E-63

548

4E-57

310

2E-29

Solyc03g121540.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6368773863693057 functional_description:"Beta-galactosidase (AHRD V1 ***- Q9ZP11_SOLLC); contains Interpro domain(s) IPR019801 Glycoside hydrolase, family 35, conserved site IPR001944 Glycoside hydrolase, family 35 IPR000922 D-galactoside/L-rhamnose binding SUEL lectin " 2

Les.1007.1.A1_at

117

3

Les.1032.2.S1_at

521

4

Les.1054.1.S1_at

338

5

Les.1058.1.S1_at

487

6

Les.1064.1.S1_at

520

7

Les.1073.1.S1_at

473

8

Les.1077.1.S1_at

345

9

Les.1081.1.S1_at

311

******* Solyc08g074240.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5552184055524554 functional_description:"40S ribosomal protein S6 (AHRD V1 ***- B6T1H0_MAIZE); contains Interpro domain(s) IPR014401 Ribosomal protein S6, eukaryotic " Solyc09g065520.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:5922973259238675 functional_description:"Homocysteine smethyltransferase (AHRD V1 **** B9GSK5_POPTR); contains Interpro domain(s) IPR003726 Homocysteine Smethyltransferase " Solyc00g085070.1.1 genomic_reference:SL2.31ch00 evidence_code:10F0H1E1IEG gene_region:1518546615188655 functional_description:"Squalene monooxygenase (AHRD V1 ***- Q506K3_DATIN); contains Interpro domain(s) IPR013698 Squalene epoxidase " Solyc04g078700.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6098360460986485 functional_description:"Receptor-like protein kinase (AHRD V1 ***- Q0WPA7_ARATH); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc10g086190.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6442784564432061 functional_description:"Adenosine kinase (AHRD V1 ***- D2D2Z6_GOSHI); contains Interpro domain(s) IPR001805 Adenosine kinase " Solyc02g078150.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3750865637509771 functional_description:"Plant-specific domain TIGR01615 family protein (AHRD V1 *-*B6UDN7_MAIZE); contains Interpro domain(s) IPR006502 Protein of unknown function DUF506, plant " Solyc09g092080.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6658093266583132 functional_description:"50S ribosomal protein L7Ae (AHRD V1 **-- B2WJB2_PYRTR); contains Interpro domain(s) IPR004038 Ribosomal protein L7Ae/L30e/S12e/Gadd45 "

Table S1 List of differentially expressed genes in rin mutant. 10

Les.109.1.S1_at

550

11

Les.113.1.S1_at

329

12

Les.1175.2.S1_at

118

13

Les.119.1.S1_at

589

14

Les.1192.1.A1_at

214

15

Les.1192.2.S1_at

141

16

Les.12.1.S1_at

543

17

Les.1205.2.S1_at

452

18

Les.1219.1.A1_at

132

19

Les.122.1.S1_at

505

20

Les.123.1.S1_at

540

21

Les.1230.1.A1_at

112

Solyc02g084720.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4239695342402547 functional_description:"Beta-galactosidase (AHRD V1 ***- Q9LLS9_SOLLC); contains Interpro domain(s) IPR019801 Glycoside hydrolase, family 35, conserved site IPR001944 Glycoside hydrolase, family 35 IPR000922 D-galactoside/L-rhamnose binding SUEL lectin " Solyc03g116510.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H0E0IEG gene_region:5996030059960581 functional_description:"Unknown Protein (AHRD V1)" Solyc03g025670.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:74920747493227 functional_description:"PAR-1c protein (AHRD V1 ***- Q43589_TOBAC); contains Interpro domain(s) IPR009489 PAR1 " Solyc01g094690.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7789789977900251 functional_description:"Aquaporin (AHRD V1 ***- Q40266_MESCR); contains Interpro domain(s) IPR012269 Aquaporin " ******* Solyc02g089080.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4556139945563495 functional_description:"Rapid alkalinization factor 5 (AHRD V1 *-*- Q6DN46_SOLCH)" Solyc06g068160.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3863050438632044 functional_description:"5&apos-AMP-activated protein kinase subunit gamma-3 (AHRD V1 **-B1PM77_SHEEP); contains Interpro domain(s) IPR000644 Cystathionine beta-synthase, core " Solyc10g008680.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E0IEG gene_region:27596992761076 functional_description:"Malonyl CoA anthocyanin 3-O-glucoside-6&apos&apos-O-malonyltransferase (AHRD V1 **-* Q8GSN8_9ASTR); contains Interpro domain(s) IPR003480 Transferase " ******* Solyc02g082920.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4112905541129950 functional_description:"Endochitinase (Chitinase) (AHRD V1 **** Q43184_SOLTU); contains Interpro domain(s) IPR000726 Glycoside hydrolase, family 19, catalytic " Solyc09g011630.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:48893764890402 functional_description:"Glutathione S-transferaselike protein (AHRD V1 **** A8DUB0_SOLLC); contains Interpro domain(s) IPR004046 Glutathione S-transferase, C-terminal " *******

207

4E-17

397

1E-39

199

1E-16

976

1E-106

*******

*******

222

2E-19

856

2E-92

483

2E-49

*******

*******

702

1E-74

786

3E-84

*******

*******


Les.1258.1.S1_at

544

Solyc12g006470.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:958012-963825 functional_description:"Aminotransferase-like protein (AHRD V1 ***- Q9LIE2_ARATH); contains Interpro domain(s) IPR005814 Aminotransferase class-III " Solyc01g109140.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8795374287955326 functional_description:"Cytochrome P450 allene oxide synthase (AHRD V1 **-* B9GP05_POPTR); contains Interpro domain(s) IPR002403 Cytochrome P450, E-class, group IV " *******

444

1E-66

23

Les.129.1.S1_at

475

739

6E-79

24

Les.1291.1.A1_at

109

*******

*******

25

Les.1296.1.A1_at

125

*******

*******

570

3E-59

692

2E-73

*******

*******

397

1E-39

95

******* Solyc04g079730.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6168617461687778 functional_description:"Allene oxide synthase (AHRD V1 **** Q9M464_SOLLC); contains Interpro domain(s) IPR002403 Cytochrome P450, E-class, group IV " Solyc01g086680.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7340385873405441 functional_description:"Glutathione S-transferase (AHRD V1 ***- D8UY87_GLYSO); contains Interpro domain(s) IPR004046 Glutathione S-transferase, Cterminal " ******* Solyc07g049550.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5717273257174490 functional_description:"1-aminocyclopropane-1carboxylate oxidase (AHRD V1 **** Q94F66_SOLTU); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " *******

26

Les.13.1.S1_at

504

27

Les.131.1.S1_at

579

28

Les.1314.1.S1_at

155

29

Les.132.1.S1_at

367

30

Les.1320.1.A1_at

*******

*******

31

Les.1331.1.A1_at

112

*******

*******

*******

32

Les.1334.1.A1_at

131

*******

*******

*******

33

Les.1376.2.A1_at

124

*******

*******

34

Les.14.1.S1_at

480

672

3E-71

35

Les.1406.1.A1_at

109

******* Solyc03g006970.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:15283931530720 functional_description:"Subtilisin-like protease (AHRD V1 ***- B6UDX1_MAIZE); contains Interpro domain(s) IPR015500 Peptidase S8, subtilisin-related IPR000183 Orn/DAP/Arg decarboxylase 2 IPR000209 Peptidase S8 and S53, subtilisin, kexin, sedolisin " *******

*******

*******

36

Les.1419.2.A1_at

131

*******

*******

37

Les.1422.1.S1_at

542

******* Solyc12g088670.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6239085862394629 functional_description:"Cathepsin B-like cysteine proteinase (AHRD V1 **-- CYSP_SCHMA); contains Interpro domain(s) IPR013128 Peptidase C1A, papain IPR000169 Peptidase, cysteine peptidase active site

518

3E-53

Table S1 List of differentially expressed genes in rin mutant. IPR000668 Peptidase C1A, papain C-terminal " 38

Les.1431.1.A1_at

92

39

Les.1455.1.S1_at

286

40

Les.1459.1.A1_at

109

41

Les.1465.1.S1_at

532

42

Les.147.1.S1_at

524

43

Les.1487.1.A1_at

114

44

Les.1495.1.S1_at

280

45

Les.1498.1.S1_at

172

46

Les.150.1.S1_at

403

47

Les.1524.1.A1_at

133

48

Les.1528.2.S1_at

252

49

Les.1594.1.S1_at

530

50

Les.1596.1.A1_at

129

51

Les.1604.1.A1_at

127

52

Les.1606.1.S1_at

407

******* Solyc05g009390.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:35447073548662 functional_description:"Lipase-like protein (AHRD V1 **-- Q9LF16_ARATH); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " ******* Solyc01g106330.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8601944286030969 functional_description:"Glutamyl-tRNA(Gln) amidotransferase subunit A (AHRD V1 ***Q5L059_GEOKA); contains Interpro domain(s) IPR000120 Amidase signature enzyme " Solyc12g006140.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:694455-695820 functional_description:"Chlorophyll a-b binding protein 37, chloroplastic (AHRD V1 ***- CB26_PETSP); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " ******* Solyc01g009070.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:30757503080069 functional_description:"MYB transcription factor (AHRD V1 **-* Q9FR97_ARATH); contains Interpro domain(s) IPR015495 Myb transcription factor " Solyc06g084540.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4592360645924347 functional_description:"Universal stress protein (AHRD V1 ***- B4UW73_ARAHY); contains Interpro domain(s) IPR006016 UspA " Solyc03g114210.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5825722758261283 functional_description:"Protein kinase (AHRD V1 **** Q9FGB1_ARATH); contains Interpro domain(s) IPR015783 ATMRK serine/threonine protein kinase-like " ******* Solyc08g082690.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6255725162559754 functional_description:"30S ribosomal protein S6 (AHRD V1 *-*- D7DYF3_NOSA0); contains Interpro domain(s) IPR000529 Ribosomal protein S6 " Solyc08g077230.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5830698258311708 functional_description:"Two-component response regulator ARR11 (AHRD V1 *-*B6UC09_MAIZE); contains Interpro domain(s) IPR006447 Myb-like DNA-binding region, SHAQKYF class " *******

*******

*******

281

3E-32

*******

*******

675

2E-71

814

1E-87

*******

*******

303

1E-28

292

2E-27

460

9E-47

*******

*******

198

2E-16

370

4E-36

*******

*******

******* Solyc04g010250.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:3577616-

*******

*******

655

2E-69

Table S1 List of differentially expressed genes in rin mutant.

53

Les.1610.1.S1_at

527

54

Les.1650.1.A1_at

125

55

Les.1665.1.S1_at

259

56

Les.17.1.S1_at

525

57

Les.1701.1.S1_at

503

58

Les.1717.1.A1_at

127

3581636 functional_description:"Lipase-like protein (AHRD V1 **-- Q9M3D1_ARATH); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc02g089620.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4595620745957959 functional_description:"Proline dehydrogenase (AHRD V1 **** A1E289_ACTDE); contains Interpro domain(s) IPR015659 Proline oxidase " ******* Solyc03g116530.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5996658759967524 functional_description:"Glyoxalase/bleomycin resistance protein/dioxygenase (AHRD V1 ***Q2HVV5_MEDTR); contains Interpro domain(s) IPR004360 Glyoxalase/bleomycin resistance protein/dioxygenase " Solyc02g067340.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3211791932120646 functional_description:"MYB transcription factor (AHRD V1 **-* Q9SN78_ARATH); contains Interpro domain(s) IPR015495 Myb transcription factor " Solyc11g065760.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4844289048445854 functional_description:"Thymidine kinase (AHRD V1 ***- Q71F77_SOLLC); contains Interpro domain(s) IPR001267 Thymidine kinase " *******

59

Les.1719.1.A1_at

128

60

Les.1727.1.A1_at

120

61

Les.1748.1.A1_at

165

62

Les.1757.1.A1_at

112

63

Les.1762.1.S1_at

322

64

Les.18.1.S1_at

544

65

Les.181.1.A1_at

66

183

2E-14

*******

*******

382

7E-38

247

8E-22

878

5E-95

*******

*******

*******

*******

*******

*******

*******

*******

*******

*******

*******

*******

*******

536

1E-55

655

4E-69

127

******* Solyc08g007040.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:16035331605523 functional_description:"Glycine cleavage system H protein 1 (AHRD V1 ***- B6UHJ7_MAIZE); contains Interpro domain(s) IPR017453 Glycine cleavage Hprotein, subgroup " Solyc07g062530.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6245564362461072 functional_description:"Phosphoenolpyruvate carboxylase 2 (AHRD V1 ***- Q9SCB2_SOLLC); contains Interpro domain(s) IPR015813 Pyruvate/Phosphoenolpyruvate kinase, catalytic core IPR001449 Phosphoenolpyruvate carboxylase " *******

*******

*******

Les.1828.1.A1_at

132

*******

*******

*******

67

Les.1830.1.A1_at

92

*******

Les.1832.1.A1_at

205

******* Solyc09g090570.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H0E1IEG gene_region:6540889465410422 functional_description:"Proton gradient regulation 5 (AHRD V1 ***- B0F831_CUCSA)"

*******

68

203

4E-17


Les.1847.2.S1_at

536

Solyc06g005970.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:948924-955752 functional_description:"Beta-D-glucosidase (AHRD V1 ***- Q7XAS3_GOSHI); contains Interpro domain(s) IPR001764 Glycoside hydrolase, family 3, N-terminal " Solyc07g062500.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:6243897862442493 functional_description:"Cytochrome P450 (AHRD V1 ***- A9ZT56_COPJA); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc02g082420.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4068997240691606 functional_description:"Ring finger protein (AHRD V1 *-*- O49869_HORVU); contains Interpro domain(s) IPR018957 Zinc finger, C3HC4 RING-type " ******* Solyc06g051800.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3196765531968782 functional_description:"Expansin (AHRD V1 ***- O04359_SOLLC); contains Interpro domain(s) IPR007112 Expansin 45, endoglucanase-like IPR007117 Pollen allergen/expansin, C-terminal " Solyc07g066470.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6511962165122539 functional_description:"Porphobilinogen deaminase (AHRD V1 ***- B6TVP0_MAIZE); contains Interpro domain(s) IPR000860 Tetrapyrrole biosynthesis, hydroxymethylbilane synthase " Solyc09g082690.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6380788763808779 functional_description:"Early light-induced protein 7 (AHRD V1 ***- B2BJD6_RHOCT)" Solyc02g064940.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3062354730624941 functional_description:"Leucine-rich repeat receptor protein kinase EXS (AHRD V1 *--* EXS_ARATH); contains Interpro domain(s) IPR001611 Leucine-rich repeat " *******

941

1E-102

70

Les.1859.2.S1_at

247

423

1E-42

71

Les.1871.1.S1_at

458

659

1E-69

72

Les.1880.1.A1_at

110

*******

*******

73

Les.191.1.S1_at

444

674

2E-71

74

Les.1929.3.S1_at

252

212

4E-34

75

Les.1936.1.S1_at

498

652

8E-69

76

Les.1951.1.A1_at

294

495

6E-51

77

Les.1959.1.A1_at

121

78

Les.1968.1.A1_at

*******

*******

142

*******

*******

*******

79

Les.198.1.S1_s_at

278

*******

*******

80

Les.1997.1.S1_at

381

401

5E-67

81

Les.20.1.S1_at

576

849

1E-91

82

Les.2006.1.A1_at

112

******* Solyc04g048900.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:3771230137715488 functional_description:"Calreticulin 2 calciumbinding protein (AHRD V1 **** A8HMC0_CHLRE); contains Interpro domain(s) IPR009169 Calreticulin " Solyc01g097810.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8027707280284596 functional_description:"Zeta-carotene desaturase (AHRD V1 ***- Q202I0_SOLLC); contains Interpro domain(s) IPR014103 Carotene 7,8-desaturase " *******

*******

*******


Les.2012.1.S1_at

494

84

Les.2026.1.S1_at

507

85

Les.204.1.S1_at

537

86

Les.2040.1.A1_at

127

87

Les.2090.1.S1_at

259

88

Les.2092.1.S1_at

413

89

Les.2119.1.A1_s_at

91

90

Les.2128.1.S1_at

505

91

Les.213.1.S1_at

405

92

Les.2137.1.S1_at

567

93

Les.214.1.S1_at

389

94

Les.2168.1.S1_at

375

Solyc04g054740.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5232873352331512 functional_description:"Inositol-3-phosphate synthase (AHRD V1 ***- C4PW06_ARATH); contains Interpro domain(s) IPR002587 Myo-inositol-1-phosphate synthase " Solyc10g008400.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:25343042534969 functional_description:"RING finger protein 5 (AHRD V1 *--- B6TI40_MAIZE); contains Interpro domain(s) IPR018957 Zinc finger, C3HC4 RING-type " Solyc07g056140.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6131708661321353 functional_description:"Glucose-1-phosphate adenylyltransferase (AHRD V1 **** D5L5Q9_SOLLC); contains Interpro domain(s) IPR011831 Glucose-1phosphate adenylyltransferase " ******* Solyc01g108020.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8715772187162057 functional_description:"Thioredoxin m (AHRD V1 ***- B9HS17_POPTR); contains Interpro domain(s) IPR015467 Thioredoxin, core " Solyc02g080530.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3931795239319241 functional_description:"Peroxidase (AHRD V1 **** C7DYB2_9ERIC); contains Interpro domain(s) IPR002016 Haem peroxidase, plant/fungal/bacterial " ******* Solyc11g045670.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:4036765340370080 functional_description:"Palmitoyltransferase PFA4 (AHRD V1 *-** PFA4_NEUCR); contains Interpro domain(s) IPR001594 Zinc finger, DHHC-type " Solyc06g005470.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H0E1IEG gene_region:482823-484028 functional_description:"Metallothionein-like protein type 2 (AHRD V1 --*- MT2Z_SOLLC); contains Interpro domain(s) IPR000347 Plant metallothionein, family 15 " Solyc07g008620.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:35695713572666 functional_description:"Leucine Rich Repeat family protein expressed (AHRD V1 **-Q2R2L4_ORYSJ); contains Interpro domain(s) IPR013210 Leucine-rich repeat, N-terminal " Solyc01g103390.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8376104483763253 functional_description:"Flavin oxidoreductase/NADH oxidase (AHRD V1 **-A0YMI2_LYNSP); contains Interpro domain(s) IPR001155 NADH:flavin oxidoreductase/NADH oxidase, N-terminal " Solyc08g013670.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:3047164-

380

3E-37

766

1E-89

383

6E-63

*******

*******

370

2E-36

603

2E-63

*******

*******

389

2E-38

119

5E-16

735

2E-78

595

2E-62

479

4E-49


95

Les.217.1.S1_at

381

96

Les.2187.1.A1_at

149

97

Les.22.1.S1_at

534

98

Les.2203.1.S1_at

486

99

Les.2209.1.A1_at

108

100

Les.221.1.S1_at

503

101

Les.2229.1.S1_at

465

102

Les.224.1.S1_at

261

103

Les.2256.1.S1_at

439

104

Les.2257.1.A1_at

126

105

Les.2264.1.S1_at

422

106

Les.2265.1.S1_at

399

107

Les.2278.1.S1_at

486

3048024 functional_description:"Photosystem I reaction center subunit (AHRD V1 ***- D2K7Z2_TOBAC); contains Interpro domain(s) IPR008796 Photosystem I reaction centre subunit N " Solyc07g008110.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:28312492832708 functional_description:"Blue copper protein (Fragment) (AHRD V1 *--- O82576_MAIZE); contains Interpro domain(s) IPR003245 Plastocyanin-like " ******* Solyc10g086220.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6444414864445480 functional_description:"Flavin oxidoreductase/NADH oxidase (AHRD V1 **-A0YMI2_LYNSP); contains Interpro domain(s) IPR001155 NADH:flavin oxidoreductase/NADH oxidase, N-terminal " Solyc04g012120.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:44287554429971 functional_description:"14-3-3 protein beta/alpha1 (AHRD V1 **-- 143B1_ONCMY); contains Interpro domain(s) IPR000308 14-3-3 protein " ******* Solyc02g081190.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3982897539830346 functional_description:"1-aminocyclopropane-1carboxylate oxidase (AHRD V1 ***- Q9ZWP2_SOLLC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc11g006970.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:14777941483280 functional_description:"Unknown protein DS12 from 2D-PAGE of leaf, chloroplastic (AHRD V1 **-UP12_ORYSJ)" ******* Solyc03g111730.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5643304856434520 functional_description:"Cathepsin B-like cysteine proteinase (AHRD V1 **-* CYSP_SCHMA); contains Interpro domain(s) IPR013128 Peptidase C1A, papain " ******* Solyc06g051010.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3059319730594969 functional_description:"Peptide-N4-(N-acetylbeta- glucosaminyl)asparagine amidase A (AHRD V1 ***B2W0X1_PYRTR)" Solyc11g008680.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:28597152863853 functional_description:"Acyl- (AHRD V1 ***Q4JIJ4_9ROSI); contains Interpro domain(s) IPR005067 Fatty acid desaturase, type 2 " Solyc02g083860.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:41700154-

271

6E-25

*******

*******

785

3E-84

561

3E-58

*******

*******

612

3E-64

696

5E-74

*******

*******

689

3E-73

*******

*******

504

8E-52

629

2E-66

654

4E-69


108

Les.2287.1.S1_at

247

109

Les.230.1.S1_at

279

110

Les.231.1.S1_at

347

111

Les.2316.2.A1_at

118

112

Les.2328.1.A1_at

133

113

Les.233.1.S1_at

499

114

Les.2332.1.A1_at

133

115

Les.2341.1.A1_at

104

116

Les.24.1.S1_at

572

117

Les.2403.2.S1_at

363

118

Les.2409.1.S1_at

437

119

Les.241.2.S1_at

313

41701928 functional_description:"Flavanone 3-hydroxylase (AHRD V1 ***- A9ZMI9_TOBAC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc09g010110.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:34941423498773 functional_description:"Chaperone protein dnaJlike (AHRD V1 **-- Q6H3Y3_ORYSJ)" Solyc09g011670.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:49147804916004 functional_description:"Universal stress protein family protein (AHRD V1 ***- D7LUP3_ARALY); contains Interpro domain(s) IPR006016 UspA " Solyc09g082060.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6329918963303301 functional_description:"Cysteine synthase (AHRD V1 **** Q3LAG5_TOBAC); contains Interpro domain(s) IPR005859 Cysteine synthase A " ******* ******* Solyc07g047850.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5640654956407460 functional_description:"Chlorophyll a-b binding protein 4, chloroplastic (AHRD V1 **** CB24_SOLLC); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc09g005480.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H0E1IEG gene_region:332534-333942 functional_description:"F-box family protein (AHRD V1 ***- B9HCS6_POPTR); contains Interpro domain(s) IPR001810 Cyclin-like F-box " ******* Solyc03g019790.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:67171766722581 functional_description:"Alpha-galactosidase (AHRD V1 **** Q9SP05_SOLLC); contains Interpro domain(s) IPR013785 Aldolase-type TIM barrel " Solyc10g085870.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6423757164239031 functional_description:"UDP-glucosyltransferase family 1 protein (AHRD V1 ***- C6KI43_CITSI); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " Solyc05g007490.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:20474712052071 functional_description:"Dehydration-responsive family protein (AHRD V1 ***- D7KPN7_ARALY); contains Interpro domain(s) IPR004159 Protein of unknown function DUF248, methyltransferase putative " Solyc02g077990.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3737452837377786 functional_description:"30S ribosomal protein S5 (AHRD V1 ***- B6TT32_MAIZE); contains Interpro

176

5E-14

314

5E-30

232

2E-20

*******

*******

*******

*******

881

2E-95

240

2E-21

*******

*******

706

5E-75

578

1E-60

323

8E-31

484

1E-49


120

Les.2457.1.A1_at

172

121

Les.2474.2.A1_at

116

122

Les.2476.1.S1_at

261

123

Les.2478.1.S1_a_at

32

124

Les.248.1.S1_a_at

376

125

Les.2494.2.A1_at

122

126

Les.2504.1.A1_at

149

127

Les.2512.2.S1_at

389

128

Les.2529.1.A1_at

134

129

Les.2540.3.S1_at

464

130

Les.2544.1.A1_at

130

131

Les.2545.1.S1_at

564

132

Les.255.1.A1_at

535

133

Les.2559.3.S1_at

322

domain(s) IPR005712 Ribosomal protein S5, bacterial-type " *******

*******

*******

******* Solyc07g054780.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:6030920460309455 functional_description:"Wound induced protein (AHRD V1 ***- B6T0U0_MAIZE)" ******* Solyc01g097270.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7994123279942225 functional_description:"Chitinase (Fragment) (AHRD V1 *--- Q38777_ALLSA); contains Interpro domain(s) IPR000726 Glycoside hydrolase, family 19, catalytic IPR001153 Barwin " *******

*******

*******

275

2E-25

*******

*******

619

3E-65

*******

*******

******* Solyc10g083650.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6276187462762560 functional_description:"Peroxiredoxin ahpC/TSA family (AHRD V1 **-- Q1YGN4_MOBAS); contains Interpro domain(s) IPR013740 Redoxin " Solyc07g049660.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5735083657352364 functional_description:"Acetyl coenzyme A cis3-hexen-1-ol acetyl transferase (AHRD V1 **-* Q9SRQ2_ARATH); contains Interpro domain(s) IPR003480 Transferase " Solyc07g041490.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5063213850632941 functional_description:"Stress responsive alphabeta barrel domain protein (AHRD V1 *-*C7QRA6_CYAP0); contains Interpro domain(s) IPR013097 Stress responsive alpha-beta barrel " ******* Solyc02g070540.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3486422634866590 functional_description:"Os01g0611000 protein (Fragment) (AHRD V1 ***- Q0JLB5_ORYSJ); contains Interpro domain(s) IPR006946 Protein of unknown function DUF642 " Solyc04g076960.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5949625159502963 functional_description:"Sucrose transporter (AHRD V1 **** Q9FVJ6_SOLLC); contains Interpro domain(s) IPR005989 Sucrose/H+ symporter, plant " Solyc00g011890.1.1 genomic_reference:SL2.31ch00 evidence_code:10F0H1E1IEG gene_region:1033360710350086 functional_description:"Galactokinase like protein (AHRD V1 **** O23461_ARATH); contains Interpro domain(s) IPR012369 Galactokinase, glycosyltransferase "

*******

*******

399

1E-39

134

2E-13

720

9E-77

*******

*******

565

1E-58

368

7E-36

416

8E-42


Les.2582.1.S1_at

402

135

Les.2587.1.A1_at

132

136

Les.259.2.S1_a_at

545

137

Les.2591.1.S1_at

561

138

Les.2626.1.S1_at

501

139

Les.263.1.S1_at

460

140

Les.2642.1.S1_at

419

141

Les.2643.1.S1_at

181

142

Les.2649.1.S1_at

518

143

Les.2668.1.S1_at

329

144

Les.2672.1.S1_x_at

549

Solyc05g054720.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6372702863729336 functional_description:"Tic20-like protein (AHRD V1 ***- Q2V9A0_SOLTU); contains Interpro domain(s) IPR005691 Chloroplast protein import component Tic20 " ******* Solyc03g123760.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6455471264561567 functional_description:"Phytoene desaturase (AHRD V1 **** Q3S1N6_SOLLC); contains Interpro domain(s) IPR014102 Phytoene desaturase " Solyc01g060020.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:6222485862226598 functional_description:"Beta-glucanase (AHRD V1 ***- Q53X08_NICPL); contains Interpro domain(s) IPR000490 Glycoside hydrolase, family 17 " Solyc03g093360.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4807904248079913 functional_description:"Wound/stress protein (AHRD V1 **-- Q672Q3_SOLLC); contains Interpro domain(s) IPR001024 Lipoxygenase, LH2 " Solyc05g005560.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:402807-404944 functional_description:"BURP domain-containing protein (Fragment) (AHRD V1 *--- C1PI44_ARATH); contains Interpro domain(s) IPR004873 BURP " Solyc03g119210.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6192491561925196 functional_description:"Lipid transfer protein (AHRD V1 ***- Q42158_ARATH); contains Interpro domain(s) IPR013770 Plant lipid transfer protein and hydrophobic protein, helical " Solyc03g031890.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H0E1IEG gene_region:86318848633967 functional_description:"Cold induced protein-like (AHRD V1 *--- Q94JH8_ORYSJ)" Solyc10g078550.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5966415159667193 functional_description:"Glutamate dehydrogenase (AHRD V1 **** Q8L6A0_TOBAC); contains Interpro domain(s) IPR014362 Glutamate dehydrogenase " Solyc01g107390.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8671013786712151 functional_description:"Auxin-responsive GH3 product (AHRD V1 ***- Q05680_SOYBN); contains Interpro domain(s) IPR004993 GH3 auxin-responsive promoter " Solyc06g062540.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3585456435855665 functional_description:"Phosphatase (AHRD V1 ***- D2V497_NAEGR); contains Interpro domain(s) IPR016965 Pyridoxal phosphate phosphatase, PHOSPHO2

529

9E-55

*******

*******

514

9E-53

543

4E-56

740

5E-79

476

2E-48

396

3E-39

300

2E-28

326

6E-51

501

1E-51

888

4E-96

Table S1 List of differentially expressed genes in rin mutant. " 145

Les.2681.2.S1_at

309

146

Les.2688.1.S1_at

508

147

Les.269.1.S1_at

528

148

Les.2701.1.A1_at

133

149

Les.2702.1.S1_a_at

532

150

Les.2703.1.S1_at

465

151

Les.2713.1.A1_at

132

152

Les.2747.2.S1_at

248

153

Les.275.3.S1_at

148

154

Les.2763.1.S1_at

277

155

Les.2769.1.A1_at

236

156

Les.278.1.S1_at

240

Solyc02g091280.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4720286047207102 functional_description:"ATP-dependent Clp protease proteolytic subunit (AHRD V1 **** B9H362_POPTR); contains Interpro domain(s) IPR001907 Peptidase S14, ClpP " Solyc04g081870.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6332758263329829 functional_description:"Expansin (AHRD V1 ***- Q9FVH0_SOLLC); contains Interpro domain(s) IPR002963 Expansin " Solyc03g082420.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4589943245900241 functional_description:"Heat shock protein (AHRD V1 ***- A9QVH3_9FABA); contains Interpro domain(s) IPR002068 Heat shock protein Hsp20 " ******* Solyc03g083910.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4739842347402347 functional_description:"Acid betafructofuranosidase (AHRD V1 **-- Q575T1_WHEAT); contains Interpro domain(s) IPR001362 Glycoside hydrolase, family 32 " Solyc03g123830.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6459419464596833 functional_description:"Phosphoglycerate dehydrogenase (AHRD V1 **** D2D316_GOSHI); contains Interpro domain(s) IPR015508 D-3phosphogylcerate Dehydrogenase " ******* Solyc09g061840.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:5605421856059772 functional_description:"3-ketoacyl CoA thiolase 1 (AHRD V1 **** C8YNG6_PETHY); contains Interpro domain(s) IPR002155 Thiolase " Solyc03g111970.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5659782056599578 functional_description:"Cytochrome P450 (AHRD V1 ***- O04163_NEPRA); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc08g006880.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:14227611449040 functional_description:"ABC transporter C family member 2 (AHRD V1 **-- AB2C_ARATH); contains Interpro domain(s) IPR001140 ABC transporter, transmembrane region " Solyc12g099560.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6500467665013653 functional_description:"Arginine Nmethyltransferase family protein (AHRD V1 ***D7L611_ARALY)" Solyc09g010430.1.1 genomic_reference:SL2.31ch09

441

1E-44

188

5E-15

829

3E-89

*******

*******

514

9E-53

719

1E-76

*******

*******

395

2E-39

241

2E-21

371

1E-36

162

2E-12

395

2E-39


157

Les.2792.1.A1_at

99

158

Les.28.2.S1_a_at

272

159

Les.2809.1.S1_at

429

160

Les.281.3.S1_at

167

161

Les.2810.2.S1_at

562

162

Les.2813.1.S1_at

441

163

Les.2822.3.S1_at

229

164

Les.2831.1.S1_at

499

165

Les.2845.2.S1_at

241

166

Les.2850.1.S1_at

395

167

Les.2863.1.S1_at

456

evidence_code:10F0H0E0IEG gene_region:38005983800861 functional_description:"Unknown Protein (AHRD V1)" ******* Solyc11g069760.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E0IEG gene_region:5145934851459899 functional_description:"High affinity nitrate transporter protein (AHRD V1 ***- Q84MZ8_TOBAC); contains Interpro domain(s) IPR016196 Major facilitator superfamily, general substrate transporter " Solyc12g009930.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:30968473098202 functional_description:"UDPglucuronosyltransferase 1-6 (AHRD V1 *-*UD16_MOUSE); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDP-glucosyltransferase " Solyc03g117870.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6093455260937771 functional_description:"4-coumarate CoA ligase (AHRD V1 **** Q0GZS1_9BORA); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc07g006030.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:867276880835 functional_description:"Protein TIF31 homolog (AHRD V1 *--- TIF31_COCIM); contains Interpro domain(s) IPR011990 Tetratricopeptide-like helical " Solyc06g074670.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4260074842604401 functional_description:"Bifunctional polymyxin resistance arnA protein (AHRD V1 ***B6TQB1_MAIZE); contains Interpro domain(s) IPR001509 NAD-dependent epimerase/dehydratase " Solyc01g059930.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:6216167862163893 functional_description:"Universal stress protein (AHRD V1 ***- D6BRD7_9ROSI); contains Interpro domain(s) IPR006016 UspA " Solyc03g114150.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5822308558227400 functional_description:"Aldehyde dehydrogenase (AHRD V1 **** Q1AFF6_9ROSI); contains Interpro domain(s) IPR015590 Aldehyde dehydrogenase " Solyc03g118200.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6118871561198729 functional_description:"Copine-3 (AHRD V1 ***- B6SK39_MAIZE); contains Interpro domain(s) IPR010734 Copine " Solyc07g009230.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:42632374264219 functional_description:"Unknown Protein (AHRD V1)" *******

*******

*******

352

2E-34

660

6E-70

279

6E-26

307

6E-51

739

5E-79

379

2E-37

844

4E-91

407

9E-41

407

1E-40

*******

*******


Les.2866.1.A1_at

487

169

Les.2876.2.S1_at

328

170

Les.288.1.S1_at

396

171

Les.2886.2.S1_at

242

172

Les.2897.1.S1_at

403

173

Les.2899.1.S1_at

480

174

Les.290.1.S1_at

522

175

Les.2909.2.S1_at

290

176

Les.2917.1.S1_at

293

177

Les.2917.2.S1_at

155

178

Les.2921.1.S1_at

357

Solyc10g054840.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H0E1IEG gene_region:5147050951471687 functional_description:"Aquaporin (AHRD V1 ***- C8CE50_FRAAN); contains Interpro domain(s) IPR000425 Major intrinsic protein " Solyc09g009100.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:24467462448992 functional_description:"Heat stress transcription factor A3 (AHRD V1 ***- D1M7W9_SOLLC); contains Interpro domain(s) IPR000232 Heat shock factor (HSF)type, DNA-binding " Solyc10g006880.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:13057781308341 functional_description:"NAC domain protein (AHRD V1 ***- Q56UP7_SOLLC); contains Interpro domain(s) IPR003441 No apical meristem (NAM) protein " Solyc02g036370.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:2130889021310939 functional_description:"MYB transcription factor (Fragment) (AHRD V1 **-* A1DR85_CATRO); contains Interpro domain(s) IPR006447 Myb-like DNA-binding region, SHAQKYF class " Solyc07g015860.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:56267805628870 functional_description:"Peptide deformylase (AHRD V1 **** B9GKW9_POPTR); contains Interpro domain(s) IPR000181 Formylmethionine deformylase " Solyc03g111720.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5643191256432586 functional_description:"Peptide methionine sulfoxide reductase msrA (AHRD V1 **** D7E9W5_METEZ); contains Interpro domain(s) IPR002569 Methionine sulphoxide reductase A " Solyc08g066240.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5193126251933329 functional_description:"Decarboxylase family protein (AHRD V1 ***- A7GHE9_CLOBL); contains Interpro domain(s) IPR002129 Pyridoxal phosphatedependent decarboxylase " Solyc07g055060.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:6051266060519365 functional_description:"Phosphoenolpyruvate carboxylase 1 (AHRD V1 ***- O23946_GOSHI); contains Interpro domain(s) IPR015813 Pyruvate/Phosphoenolpyruvate kinase, catalytic core IPR001449 Phosphoenolpyruvate carboxylase " *******

572

1E-59

294

1E-27

569

2E-59

388

1E-38

462

5E-47

717

2E-76

735

2E-78

494

7E-51

*******

*******

******* Solyc12g096500.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6373668363737850 functional_description:"CONSTANS-like protein (AHRD V1 ***- Q0MQL9_SOLTU); contains Interpro domain(s) IPR010402 CCT domain "

*******

*******

479

4E-49


Les.2942.1.S1_at

298

180

Les.2946.2.S1_at

388

181

Les.2971.2.A1_at

133

182

Les.2985.1.A1_at

141

183

Les.300.2.S1_at

243

184

Les.3007.1.S1_at

174

185

Les.3014.1.S1_at

371

186

Les.3016.1.S1_at

534

187

Les.3034.1.S1_at

504

188

Les.3037.1.S1_at

272

189

Les.3040.2.A1_at

84

190

Les.3046.1.S1_at

546

191

Les.3052.1.S1_at

202

******* Solyc01g006400.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:10214601023046 functional_description:"Cysteine-rich extensin-like protein-4 (AHRD V1 *-*- Q08197_TOBAC)" ******* Solyc04g040160.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:3107572431080423 functional_description:"Pheophorbide a oxygenase (AHRD V1 **-* B6ST74_MAIZE); contains Interpro domain(s) IPR013626 Pheophorbide a oxygenase " Solyc02g092000.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4780095747804484 functional_description:"Unknown Protein (AHRD V1)" Solyc07g062190.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6221853062222409 functional_description:"50S ribosomal protein L13 (AHRD V1 ***- B6SVH3_MAIZE); contains Interpro domain(s) IPR005823 Ribosomal protein L13, bacterialtype " Solyc06g048410.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:2749735227499531 functional_description:"Superoxide dismutase (AHRD V1 **** Q7YK44_SOLLC); contains Interpro domain(s) IPR019833 Manganese/iron superoxide dismutase, binding site IPR001189 Manganese/iron superoxide dismutase " Solyc07g063600.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6326671663268089 functional_description:"Chlorophyll a-b binding protein 13, chloroplastic (AHRD V1 ***- CB23_SOLLC); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc11g020960.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:1299640312996921 functional_description:"Proteinase inhibitor II (AHRD V1 ***- B3F0C1_TOBAC); contains Interpro domain(s) IPR003465 Proteinase inhibitor I20, Pin2 " Solyc10g006290.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:946986-949740 functional_description:"Endoribonuclease L-PSP family protein (AHRD V1 **-* D7LAZ0_ARALY); contains Interpro domain(s) IPR019897 YjgF-like protein, conserved site " ******* Solyc06g075010.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4292979142934057 functional_description:"chaperonin (AHRD V1 ***- B2IXD2_NOSP7); contains Interpro domain(s) IPR001844 Chaperonin Cpn60 " Solyc06g071960.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:40717758-

*******

*******

430

2E-43

*******

*******

151

4E-11

413

2E-41

280

5E-26

604

1E-63

540

8E-56

792

5E-85

447

2E-45

*******

*******

586

4E-61

329

1E-31


192

Les.3054.1.S1_at

509

193

Les.3065.1.S1_at

131

194

Les.3069.1.S1_at

444

195

Les.3071.2.S1_at

207

196

Les.3072.1.S1_at

274

197

Les.3073.1.S1_at

397

198

Les.3085.1.S1_at

327

199

Les.3090.1.S1_at

513

200

Les.3113.2.S1_at

116

40720570 functional_description:"Nucleoside diphosphate kinase (AHRD V1 **** B9RAM1_RICCO); contains Interpro domain(s) IPR001564 Nucleoside diphosphate kinase, core " Solyc12g011450.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:42634904264596 functional_description:"Chlorophyll a-b binding protein 13, chloroplastic (AHRD V1 ***- CB23_SOLLC); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc10g009080.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H0E1IEG gene_region:31084453110205 functional_description:"Squamosa promoter binding-like protein (AHRD V1 ***- Q0PY35_SOLLC); contains Interpro domain(s) IPR017238 Squamosa promoter-binding protein " Solyc03g043920.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E0IEG gene_region:1160375311606459 functional_description:"Alpha-6galactosyltransferase (AHRD V1 **-- Q5TIN0_MEDTR); contains Interpro domain(s) IPR008630 Galactosyl transferase " Solyc07g017610.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:76681657679799 functional_description:"Saccharopine dehydrogenase (NAD(+) L-glutamate-forming) (AHRD V1 *-** C7PUW7_CHIPD); contains Interpro domain(s) IPR005097 Saccharopine dehydrogenase " Solyc02g020940.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:1108232911083800 functional_description:"Glyceraldehyde-3phosphate dehydrogenase (AHRD V1 **** D7UNZ5_BRARC); contains Interpro domain(s) IPR000173 Glyceraldehyde 3-phosphate dehydrogenase " Solyc06g060340.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3471188334713649 functional_description:"Chloroplast photosystem II-associated protein (AHRD V1 ***- A8HPM2_CHLRE); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc11g013110.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:59614005965640 functional_description:"Anthocyanidin synthase (AHRD V1 **** B2M0X8_GINBI); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc01g086820.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7352510673525516 functional_description:"Histone H3 (AHRD V1 ***- D8L9K7_WHEAT); contains Interpro domain(s) IPR000164 Histone H3 " Solyc06g005750.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:785326-789721 functional_description:"Sterol 4-alpha-methyl-oxidase 2

880

3E-95

217

1E-18

389

2E-38

355

9E-35

258

2E-23

520

9E-54

473

2E-48

321

2E-30

223

2E-19


201

Les.312.1.A1_at

118

202

Les.3122.1.S1_a_at

541

203

Les.3122.2.A1_a_at

154

204

Les.3123.1.S1_at

354

205

Les.3124.2.S1_at

330

206

Les.3140.3.S1_at

226

207

Les.3150.1.S1_at

312

208

Les.3152.2.A1_at

129

209

Les.3154.2.S1_at

318

210

Les.3157.1.S1_at

485

211

Les.3164.1.A1_at

158

212

Les.3168.1.S1_at

549

(AHRD V1 **** D7KH21_ARALY); contains Interpro domain(s) IPR006694 Fatty acid hydroxylase " ******* Solyc07g064170.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6365808763660013 functional_description:"Pectinesterase (AHRD V1 ***- B9RXQ4_RICCO); contains Interpro domain(s) IPR018040 Pectinesterase, active site IPR000070 Pectinesterase, catalytic " Solyc07g064170.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6365808763660013 functional_description:"Pectinesterase (AHRD V1 ***- B9RXQ4_RICCO); contains Interpro domain(s) IPR018040 Pectinesterase, active site IPR000070 Pectinesterase, catalytic " Solyc03g115980.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5958928959590683 functional_description:"Geranylgeranyl reductase (AHRD V1 ***- Q1ZYL0_OLEEU); contains Interpro domain(s) IPR011774 Geranylgeranyl reductase, plants and cyanobacteria " Solyc03g121880.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6396650463970518 functional_description:"Protein phosphatase 2C (AHRD V1 ***- A5A6P8_WHEAT); contains Interpro domain(s) IPR015655 Protein phosphatase 2C " Solyc09g061840.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:5605421856059772 functional_description:"3-ketoacyl CoA thiolase 1 (AHRD V1 **** C8YNG6_PETHY); contains Interpro domain(s) IPR002155 Thiolase " Solyc07g042250.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5268429852686250 functional_description:"chaperonin (AHRD V1 *-*- B4WMS9_9SYNE); contains Interpro domain(s) IPR017416 Chaperonin 21, chloroplast IPR018369 Chaperonin Cpn10, conserved site " ******* Solyc06g065390.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:3719743037200275 functional_description:"50S ribosomal protein L21 (AHRD V1 *-*- B6U3Z0_MAIZE); contains Interpro domain(s) IPR001787 Ribosomal protein L21 " Solyc03g097870.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5363690753639045 functional_description:"MtN3-like protein (AHRD V1 **-- Q9LUE3_ARATH); contains Interpro domain(s) IPR018179 RAG1-activating protein 1 homologue " ******* Solyc05g051850.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6140867061412307 functional_description:"Inositol-3-phosphate

*******

*******

470

1E-47

214

2E-18

613

1E-64

171

2E-13

310

2E-29

369

2E-36

*******

*******

453

4E-46

283

4E-26

*******

*******

381

2E-37


213

Les.317.1.S1_at

296

214

Les.3171.4.A1_at

490

215

Les.3186.3.A1_at

127

216

Les.3187.1.S1_at

498

217

Les.3209.1.S1_at

229

218

Les.3210.1.S1_at

385

219

Les.3210.2.A1_a_at

61

220

Les.3210.2.A1_at

463

221

Les.3213.2.S1_at

173

222

Les.3217.3.S1_s_at

133

223

Les.323.1.S1_at

395

synthase (AHRD V1 ***- C4PW06_ARATH); contains Interpro domain(s) IPR002587 Myo-inositol-1-phosphate synthase " Solyc06g051750.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3179324231799993 functional_description:"Cytochrome P450 (AHRD V1 ***- Q70Z22_TOBAC); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc03g031860.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:86079478611248 functional_description:"Phytoene synthase (AHRD V1 **** A1Z0Z4_SOLLC); contains Interpro domain(s) IPR002060 Squalene/phytoene synthase " ******* Solyc10g007600.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:18972731900788 functional_description:"L-lactate dehydrogenase (AHRD V1 ***- LLDD_VIBPA); contains Interpro domain(s) IPR012133 Alpha-hydroxy acid dehydrogenase, FMN-dependent " Solyc06g072240.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E0IEG gene_region:4090276740903078 functional_description:"Histone H4 (AHRD V1 ***- B6T0P4_MAIZE); contains Interpro domain(s) IPR001951 Histone H4 " Solyc07g006570.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:13832211384731 functional_description:"S8-RNase (Fragment) (AHRD V1 **-- Q5XPJ2_MALDO); contains Interpro domain(s) IPR001568 Ribonuclease T2 " ******* Solyc07g006570.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:13832211384731 functional_description:"S8-RNase (Fragment) (AHRD V1 **-- Q5XPJ2_MALDO); contains Interpro domain(s) IPR001568 Ribonuclease T2 " Solyc08g062610.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:4877701848779764 functional_description:"Cyclopropane-fatty-acylphospholipid synthase (AHRD V1 ***A9ASG7_BURM1); contains Interpro domain(s) IPR003333 Cyclopropane-fatty-acyl-phospholipid synthase " Solyc02g085950.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4329352143294237 functional_description:"Ribulose bisphosphate carboxylase small chain (AHRD V1 ***A9YTZ7_SOLTU); contains Interpro domain(s) IPR000894 Ribulose bisphosphate carboxylase, small chain " Solyc01g009860.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:43824714384269 functional_description:"NAC domain transcription factor (AHRD V1 **** Q5DM36_WHEAT); contains

540

3E-56

413

4E-41

*******

*******

383

1E-37

248

2E-22

720

6E-77

*******

*******

386

5E-38

202

5E-17

171

2E-15

674

1E-71


224

Les.3234.1.A1_at

321

225

Les.3242.1.A1_at

248

226

Les.3250.3.S1_at

212

227

Les.3266.2.S1_at

269

228

Les.3267.1.S1_at

405

229

Les.327.1.S1_at

379

230

Les.3273.1.S1_at

309

231

Les.3286.1.S1_at

545

232

Les.3292.2.S1_at

364

233

Les.3297.1.S1_at

390

234

Les.3322.1.S1_at

536

235

Les.3330.3.A1_at

119

Interpro domain(s) IPR003441 No apical meristem (NAM) protein " Solyc10g075160.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5820967558210109 functional_description:"Ferredoxin I (AHRD V1 ***- Q93XJ9_SOLTU); contains Interpro domain(s) IPR010241 Ferredoxin [2Fe-2S], plant " ******* ******* Solyc08g076970.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5807770258080209 functional_description:"Acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase (AHRD V1 **-- D4MFM7_9ENTE); contains Interpro domain(s) IPR011650 Peptidase M20, dimerisation " Solyc08g080570.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6099488860997591 functional_description:"UDP-glucose 4epimerase (AHRD V1 **** B0M3E8_PEA); contains Interpro domain(s) IPR005886 UDP-glucose 4-epimerase " Solyc07g043130.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5404714954049262 functional_description:"Os12g0117400 protein (Fragment) (AHRD V1 **-- Q0IQJ6_ORYSJ); contains Interpro domain(s) IPR004249 NPH3 " ******* Solyc07g064600.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6390121663902959 functional_description:"Endoribonuclease L-PSP family protein (AHRD V1 **-* D7LAZ0_ARALY); contains Interpro domain(s) IPR019897 YjgF-like protein, conserved site " Solyc03g065250.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:3838699638392620 functional_description:"CER1 (AHRD V1 **-B6TFH3_MAIZE); contains Interpro domain(s) IPR006694 Fatty acid hydroxylase " Solyc03g115900.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5954508059545987 functional_description:"Chlorophyll a-b binding protein P4, chloroplastic (AHRD V1 ***- CB24_PEA); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc04g015750.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:60341866039621 functional_description:"Magnesium chelatase H subunit (AHRD V1 ***- D5KXY0_VITVI); contains Interpro domain(s) IPR011771 Magnesium-chelatase, subunit H " Solyc07g045440.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5586308055864309 functional_description:"Fasciclin-like arabinogalactan protein 19 (AHRD V1 ***-

396

2E-39

*******

*******

*******

*******

425

7E-43

693

9E-74

627

3E-66

*******

*******

592

8E-62

645

2E-68

702

7E-75

766

5E-82

192

8E-16


236

Les.3343.3.S1_at

221

237

Les.3368.1.S1_at

464

238

Les.3372.1.S1_at

349

239

Les.3373.1.S1_at

263

240

Les.3383.1.S1_at

511

241

Les.3388.2.S1_at

349

242

Les.34.1.S1_at

529

243

Les.3406.1.S1_at

411

244

Les.3408.1.S1_at

339

245

Les.3409.2.S1_at

401

A9XTM4_GOSHI); contains Interpro domain(s) IPR000782 FAS1 domain " Solyc10g080610.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6116492561165959 functional_description:"Kelch-like protein 14 (AHRD V1 ***- B6T7I5_MAIZE); contains Interpro domain(s) IPR015915 Kelch-type beta propeller " Solyc07g007670.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:23167552323513 functional_description:"Purple acid phosphatase 3 (AHRD V1 **** Q6J5M8_SOLTU); contains Interpro domain(s) IPR015914 Purple acid phosphatase, N-terminal " Solyc05g005950.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:717824-719815 functional_description:"Solute carrier family 15 member 4 (AHRD V1 **-- S15A4_XENLA); contains Interpro domain(s) IPR000109 TGF-beta receptor, type I/II extracellular region " ******* Solyc03g025720.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:75160367519477 functional_description:"Long-chain-fatty-acid-CoA ligase (AHRD V1 **** C3JN12_RHOER); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc10g083400.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6254487162546364 functional_description:"Cytochrome P450 (AHRD V1 ***- B9I6T7_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc01g096190.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7904718079051643 functional_description:"Calcium-transporting ATPase (AHRD V1 ***- A8NHF4_COPC7); contains Interpro domain(s) IPR005782 ATPase, P-type, calciumtransporting " Solyc10g055810.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5289094252892092 functional_description:"Endochitinase (Chitinase) (AHRD V1 **** Q43184_SOLTU); contains Interpro domain(s) IPR016283 Glycoside hydrolase, family 19 IPR018371 Chitin-binding, type 1, conserved site IPR000726 Glycoside hydrolase, family 19, catalytic IPR001002 Chitin-binding, type 1 " Solyc00g174340.1.1 genomic_reference:SL2.31ch00 evidence_code:10F1H1E1IEG gene_region:1815524618155725 functional_description:"Pathogenesis-related protein 1b (AHRD V1 ***- Q941G6_SOLTU); contains Interpro domain(s) IPR018244 Allergen V5/Tpx-1 related, conserved site " Solyc01g091530.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7691032876911572 functional_description:"Fasciclin-like

381

9E-38

622

2E-65

459

8E-47

*******

*******

883

1E-95

595

1E-62

368

7E-36

763

7E-82

179

2E-14

611

3E-64


246

Les.3415.3.S1_at

271

247

Les.3436.2.S1_a_at

374

248

Les.344.1.A1_at

151

249

Les.3450.1.S1_at

468

250

Les.3460.1.S1_at

541

251

Les.3461.1.S1_at

509

252

Les.3465.1.S1_at

423

253

Les.3475.1.S1_at

481

254

Les.3478.1.S1_at

461

arabinogalactan protein 13 (AHRD V1 ***A9XTL8_GOSHI); contains Interpro domain(s) IPR000782 FAS1 domain " Solyc01g079470.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7102779271028166 functional_description:"CP12 (AHRD V1 ***O24136_TOBAC); contains Interpro domain(s) IPR003823 Protein of unknown function CP12 " Solyc06g061230.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:3561989335620267 functional_description:"Unknown Protein (AHRD V1); contains Interpro domain(s) IPR009632 Putative metallocarboxypeptidase inhibitor " ******* Solyc06g083230.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4503207245034730 functional_description:"GTP cyclohydrolase I (AHRD V1 **** Q8VYU3_SOLLC); contains Interpro domain(s) IPR001474 GTP cyclohydrolase I " Solyc10g083290.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6243381862439204 functional_description:"Beta-fructofuranosidase insoluble isoenzyme 2 (AHRD V1 **-- B6U1H5_MAIZE); contains Interpro domain(s) IPR018053 Glycoside hydrolase, family 32, active site IPR013148 Glycosyl hydrolases family 32, N-terminal IPR001362 Glycoside hydrolase, family 32 " Solyc09g010080.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:34767203480419 functional_description:"Beta-fructofuranosidase insoluble isoenzyme 2 (AHRD V1 **-- B6U1H5_MAIZE); contains Interpro domain(s) IPR001362 Glycoside hydrolase, family 32 " Solyc09g089610.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6470602064708395 functional_description:"Ethylene receptor (AHRD V1 **** Q5QG21_SOLLC); contains Interpro domain(s) IPR001789 Signal transduction response regulator, receiver region IPR014525 Signal transduction histidine kinase, hybrid-type, ethylene sensor IPR005467 Signal transduction histidine kinase, core " Solyc03g043890.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:1153760611539714 functional_description:"1-aminocyclopropane-1carboxylate synthase (AHRD V1 **** Q4LDM0_SOLLC); contains Interpro domain(s) IPR004839 Aminotransferase, class I and II IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site " Solyc07g049690.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5737171557377670 functional_description:"Cytochrome P450 allene oxide synthase (AHRD V1 **-- B9GP05_POPTR); contains Interpro domain(s) IPR002403 Cytochrome P450, E-class, group IV "

380

1E-37

455

3E-46

*******

*******

534

3E-55

866

1E-93

647

8E-69

660

6E-70

361

4E-35

610

5E-64


Les.3479.1.S1_at

442

256

Les.3485.1.S1_at

376

257

Les.3493.1.S1_at

503

258

Les.35.1.S1_at

519

259

Les.3500.1.S1_at

500

260

Les.3502.1.S1_at

231

261

Les.3510.1.S1_at

542

262

Les.3511.1.S1_at

333

263

Les.3525.1.S1_at

399

264

Les.3539.1.S1_at

447

Solyc12g056930.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4835833448361663 functional_description:"Sulfate transporter 2 (AHRD V1 ***- Q9AT47_SOLLC); contains Interpro domain(s) IPR001902 Sulphate anion transporter " Solyc06g008820.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:27640272770446 functional_description:"Sodium/hydrogen exchanger (AHRD V1 **** Q93YH2_SOLLC); contains Interpro domain(s) IPR018407 Na+/H+ exchanger, isoforms 1-4, conserved region " Solyc08g080130.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6063568760640611 functional_description:"Phospholipase D (AHRD V1 **** Q9XGT0_GOSHI); contains Interpro domain(s) IPR011402 Phospholipase D, plant " Solyc11g006180.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:924556-929718 functional_description:"Ethylene receptor (AHRD V1 ***C0ILN8_COFCA); contains Interpro domain(s) IPR001789 Signal transduction response regulator, receiver region IPR014525 Signal transduction histidine kinase, hybridtype, ethylene sensor IPR005467 Signal transduction histidine kinase, core " Solyc07g056580.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:6171741461723048 functional_description:"Ethylene receptor (AHRD V1 **** Q5QG25_SOLLC); contains Interpro domain(s) IPR001789 Signal transduction response regulator, receiver region IPR014525 Signal transduction histidine kinase, hybrid-type, ethylene sensor IPR005467 Signal transduction histidine kinase, core " Solyc06g062920.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3610638736108171 functional_description:"ATP binding / serinethreonine kinase (AHRD V1 **** C5DB71_VITVI); contains Interpro domain(s) IPR001245 Tyrosine protein kinase " Solyc01g067890.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:6925964769263436 functional_description:"1-deoxy-D-xylulose 5phosphate synthase 1 (AHRD V1 ***- C7U110_SOLLC); contains Interpro domain(s) IPR005474 Transketolase, Nterminal IPR005475 Transketolase, central region IPR005477 Deoxyxylulose-5-phosphate synthase " ******* Solyc04g082030.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6342682263428117 functional_description:"Ornithine decarboxylase (AHRD V1 **** Q9SXF3_TOBAC); contains Interpro domain(s) IPR002433 Ornithine decarboxylase " Solyc04g009900.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:32146943215621 functional_description:"Calcium-dependent

334

4E-32

636

3E-67

490

3E-55

241

4E-21

356

2E-34

401

4E-40

507

6E-52

*******

*******

640

1E-67

233

2E-20


265

Les.3544.1.S1_at

472

266

Les.3555.1.S1_at

399

267

Les.3563.1.S1_at

463

268

Les.3568.1.S1_at

359

269

Les.3569.1.S1_at

441

270

Les.3573.1.S1_at

536

271

Les.3574.1.S1_at

360

272

Les.3575.1.S1_at

536

273

Les.3583.1.A1_at

473

protein kinase 2 (AHRD V1 ***- B4FZS4_MAIZE); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc03g007960.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:24491872451252 functional_description:"Carotene beta-hydroxylase (AHRD V1 **** Q0GGX1_SOLLC); contains Interpro domain(s) IPR006694 Fatty acid hydroxylase " Solyc11g066430.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4928324649283668 functional_description:"Histone H2B (AHRD V1 ***- B9T301_RICCO); contains Interpro domain(s) IPR000558 Histone H2B " Solyc06g084390.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4581522345817658 functional_description:"ER auxin binding protein 1 (AHRD V1 **** Q9ZRX6_SOLLC); contains Interpro domain(s) IPR000886 Endoplasmic reticulum, targeting sequence " Solyc10g086520.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6463379664635176 functional_description:"Expansin-1 (AHRD V1 ***- Q6RX69_PETHY); contains Interpro domain(s) IPR002963 Expansin " Solyc03g031840.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:85923538594772 functional_description:"Expansin (AHRD V1 ***Q9ZP33_SOLLC); contains Interpro domain(s) IPR007112 Expansin 45, endoglucanase-like IPR007117 Pollen allergen/expansin, C-terminal " Solyc05g052050.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6154284961543553 functional_description:"Ethylene responsive transcription factor 1a (AHRD V1 **** D1MWZ3_CITLA); contains Interpro domain(s) IPR001471 Pathogenesis-related transcriptional factor and ERF, DNA-binding " Solyc06g082590.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4465553644656282 functional_description:"Ethylene responsive transcription factor 1b (AHRD V1 *-*- C0J9I8_9ROSA); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding IPR017392 Pathogenesis-related genes transcriptional activator PTI6 " Solyc02g077370.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3690119836901683 functional_description:"Ethylene-responsive transcription factor 2 (AHRD V1 ***- B6SSU7_MAIZE); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc09g090990.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6570404665705148 functional_description:"Major allergen Mal d 1

400

1E-39

445

5E-45

512

1E-52

654

2E-69

724

3E-77

636

6E-67

347

8E-34

400

1E-39

408

9E-48


274

Les.3590.1.S1_at

592

275

Les.3597.1.S1_at

509

276

Les.3601.1.S1_s_at

167

277

Les.3608.1.S1_at

355

278

Les.3610.1.S1_at

482

279

Les.3618.1.S1_at

548

280

Les.3625.1.S1_at

531

281

Les.3627.1.S1_at

529

282

Les.3630.1.S1_at

444

283

Les.3635.1.S1_at

521

(AHRD V1 ***- Q43550_MALDO); contains Interpro domain(s) IPR000916 Bet v I allergen " Solyc01g099630.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8157153681573839 functional_description:"Xyloglucan endotransglucosylase/hydrolase 5 (AHRD V1 **** C0IRG4_ACTDE); contains Interpro domain(s) IPR016455 Xyloglucan endotransglucosylase/hydrolase IPR008263 Glycoside hydrolase, family 16, active site " Solyc01g100030.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8187029781871134 functional_description:"Deoxyuridine 5&apostriphosphate nucleotidohydrolase (AHRD V1 ***D0NVQ2_PHYIN); contains Interpro domain(s) IPR008181 DeoxyUTP pyrophosphatase subfamily 1 " ******* Solyc01g006300.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:889094-891677 functional_description:"Peroxidase (AHRD V1 **** Q43774_SOLLC); contains Interpro domain(s) IPR002016 Haem peroxidase, plant/fungal/bacterial " ******* Solyc11g022590.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H0E1IEG gene_region:1456435514565032 functional_description:"Kunitz trypsin inhibitor 4 (Fragment) (AHRD V1 **** C1J5E0_POPBA); contains Interpro domain(s) IPR002160 Proteinase inhibitor I3, Kunitz legume " Solyc11g011210.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:42637084264736 functional_description:"Gibberellin regulated protein (AHRD V1 **-- A2Q374_MEDTR); contains Interpro domain(s) IPR003854 Gibberellin regulated protein " Solyc03g095900.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5102900851030368 functional_description:"1-aminocyclopropane-1carboxylate oxidase-like protein (AHRD V1 **-* Q9LTH8_ARATH); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc07g064180.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6366777463669719 functional_description:"Pectinesterase (AHRD V1 ***- B9RXQ4_RICCO); contains Interpro domain(s) IPR018040 Pectinesterase, active site IPR000070 Pectinesterase, catalytic " Solyc08g079870.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6046592160468158 functional_description:"Subtilisin-like protease (AHRD V1 **-- Q9LWA3_SOLLC); contains Interpro domain(s) IPR015500 Peptidase S8, subtilisin-related IPR000209 Peptidase S8 and S53, subtilisin, kexin, sedolisin "

757

7E-81

488

8E-50

*******

*******

459

9E-50

*******

*******

680

5E-72

422

4E-42

515

7E-53

176

9E-14

651

1E-68


Les.3637.1.S1_at

512

285

Les.3642.1.S1_at

468

286

Les.3643.1.S1_at

433

287

Les.3645.1.S1_at

414

288

Les.3649.1.S1_at

441

289

Les.3650.1.S1_at

500

290

Les.3652.1.S1_at

515

291

Les.3653.1.S1_at

420

292

Les.3654.1.S1_at

344

293

Les.3654.1.S1_at

344

Solyc06g059840.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3411922234123312 functional_description:"3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (AHRD V1 **** A1U0F1_MARAV); contains Interpro domain(s) IPR001017 Dehydrogenase, E1 component " Solyc02g091990.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4778935147791079 functional_description:"1-aminocyclopropane-1carboxylate synthase (AHRD V1 **** Q4LDM0_SOLLC); contains Interpro domain(s) IPR004839 Aminotransferase, class I and II IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site " Solyc04g081190.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6278411462786838 functional_description:"BZIP transcription factor family protein expressed (AHRD V1 ***Q8LN44_ORYSJ); contains Interpro domain(s) IPR011616 bZIP transcription factor, bZIP-1 " Solyc02g089160.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4562231245624870 functional_description:"Cytochrome P450 (AHRD V1 ***- B9N6N1_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc05g053550.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6277882362780273 functional_description:"Chalcone synthase (AHRD V1 ***- C5IWS6_NICAL); contains Interpro domain(s) IPR011141 Polyketide synthase, type III " Solyc09g091510.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6612348266125357 functional_description:"Chalcone synthase (AHRD V1 ***- Q56I79_9SOLN); contains Interpro domain(s) IPR011141 Polyketide synthase, type III " Solyc10g079860.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6065334860654505 functional_description:"Beta-1 3-glucanase (AHRD V1 ***- Q68V46_OLEEU); contains Interpro domain(s) IPR000490 Glycoside hydrolase, family 17 " Solyc04g016470.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E0IEG gene_region:73031817304630 functional_description:"Beta-1 3-glucanase (AHRD V1 ***- B2ZP01_VITRI); contains Interpro domain(s) IPR000490 Glycoside hydrolase, family 17 " Solyc10g080210.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6088250060889135 functional_description:"Polygalacturonase A (AHRD V1 **** Q9M6S2_ACTCH); contains Interpro domain(s) IPR000743 Glycoside hydrolase, family 28 " Solyc10g080210.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6088250060889135 functional_description:"Polygalacturonase A (AHRD V1 **** Q9M6S2_ACTCH); contains Interpro domain(s) IPR000743 Glycoside hydrolase, family 28 "

599

1E-69

810

3E-87

416

1E-41

742

2E-79

745

1E-79

686

9E-73

663

4E-70

715

3E-76

606

8E-64

606

8E-64


Les.3656.1.S1_at

546

295

Les.3661.1.S1_at

429

296

Les.3662.1.S1_at

524

297

Les.3666.1.S1_at

443

298

Les.3667.1.S1_at

372

299

Les.3668.1.S1_at

474

300

Les.3669.1.S1_at

362

301

Les.3673.1.S1_at

553

302

Les.3677.1.S1_at

515

Solyc08g066070.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5172786651729761 functional_description:"Exocyst complex protein EXO70 (AHRD V1 *--- EXO70_KLULA); contains Interpro domain(s) IPR004140 Exo70 exocyst complex subunit " Solyc05g050010.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:5903445059037088 functional_description:"1-aminocyclopropane-1carboxylate synthase (AHRD V1 **** Q659H5_SOLLC); contains Interpro domain(s) IPR004839 Aminotransferase, class I and II IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site " Solyc01g095080.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7821460778217128 functional_description:"1-aminocyclopropane-1carboxylate synthase (AHRD V1 **** O65209_NICGU); contains Interpro domain(s) IPR004839 Aminotransferase, class I and II IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site " Solyc09g010210.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:35979303602915 functional_description:"Endoglucanase 1 (AHRD V1 ***- B6TRZ3_MAIZE); contains Interpro domain(s) IPR008928 Six-hairpin glycosidase-like IPR012341 Sixhairpin glycosidase IPR018221 Glycoside hydrolase, family 9, active site IPR001701 Glycoside hydrolase, family 9 " Solyc08g081620.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6177762261780886 functional_description:"Endoglucanase 1 (AHRD V1 ***- B6U0P7_MAIZE); contains Interpro domain(s) IPR008928 Six-hairpin glycosidase-like IPR012341 Sixhairpin glycosidase IPR018221 Glycoside hydrolase, family 9, active site IPR001701 Glycoside hydrolase, family 9 " Solyc08g014000.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:34165093422732 functional_description:"Lipoxygenase (AHRD V1 **** Q43190_SOLTU); contains Interpro domain(s) IPR001246 Lipoxygenase, plant " Solyc12g009300.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:25751332579077 functional_description:"Sucrose synthase (AHRD V1 **** O82693_SOLLC); contains Interpro domain(s) IPR012820 Sucrose synthase, plants and cyanobacteria IPR000368 Sucrose synthase " Solyc01g008620.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:27007822702304 functional_description:"Beta-1 3-glucanase (AHRD V1 ***- Q9SYX6_TOBAC); contains Interpro domain(s) IPR000490 Glycoside hydrolase, family 17 " Solyc05g014280.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:80896688091891 functional_description:"Heat shock protein

632

2E-66

392

8E-39

540

8E-56

498

4E-51

568

2E-59

644

6E-68

467

1E-47

787

2E-84

784

4E-84


303

Les.3679.1.S1_at

516

304

Les.3683.1.S1_at

532

305

Les.3698.1.S1_at

443

306

Les.37.1.S1_at

527

307

Les.3700.1.S1_at

452

308

Les.3702.1.A1_at

420

309

Les.3725.1.S1_at

501

310

Les.3730.1.S1_at

558

311

Les.3741.1.S1_at

528

(AHRD V1 ***- A9QVH3_9FABA); contains Interpro domain(s) IPR002068 Heat shock protein Hsp20 " Solyc05g051200.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6058762760588301 functional_description:"Ethylene-responsive transcription factor 1A (AHRD V1 *-** A9P6A4_MEDTR); contains Interpro domain(s) IPR001471 Pathogenesis-related transcriptional factor and ERF, DNA-binding " Solyc08g080620.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6102039361021073 functional_description:"Osmotin-like protein (Fragment) (AHRD V1 **-- Q8S4L1_SOLNI); contains Interpro domain(s) IPR017949 Thaumatin, conserved site IPR001938 Thaumatin, pathogenesis-related " Solyc01g081380.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7310439973110518 functional_description:"Nuclear matrix protein 1 (AHRD V1 ***- Q93XE2_SOLLC); contains Interpro domain(s) IPR010604 Plant nuclear matrix 1 " Solyc02g061770.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:2786717427868748 functional_description:"Endochitinase (Chitinase) (AHRD V1 **** Q43184_SOLTU); contains Interpro domain(s) IPR000726 Glycoside hydrolase, family 19, catalytic " Solyc07g008240.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:29659432967856 functional_description:"Non-symbiotic hemoglobin protein (AHRD V1 ***- Q4VIX3_GOSHI); contains Interpro domain(s) IPR001032 Leghaemoglobin " Solyc06g008590.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:24983992501180 functional_description:"Auxin responsive protein (AHRD V1 ***- D9IQE6_CATRO); contains Interpro domain(s) IPR003311 AUX/IAA protein " Solyc02g079220.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3840974838412949 functional_description:"Solute carrier family 2, facilitated glucose transporter member 8 (AHRD V1 **** GTR8_HUMAN); contains Interpro domain(s) IPR003663 Sugar/inositol transporter " Solyc03g115890.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E0IEG gene_region:5954099159542465 functional_description:"Expansin (AHRD V1 ***- Q9FVG9_SOLLC); contains Interpro domain(s) IPR007112 Expansin 45, endoglucanase-like IPR007117 Pollen allergen/expansin, C-terminal " Solyc11g011340.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:43880064390528 functional_description:"Alcohol dehydrogenase (AHRD V1 ***- Q8KRC3_MYXXA); contains Interpro domain(s) IPR002085 Alcohol dehydrogenase superfamily, zinc-containing "

278

2E-25

712

1E-75

563

1E-58

823

1E-98

554

1E-57

457

2E-46

476

2E-48

477

2E-48

782

7E-84


Les.3742.1.S1_at

468

313

Les.3747.1.S1_at

407

314

Les.375.1.A1_at

125

315

Les.3750.1.S1_at

552

316

Les.3752.1.S1_at

196

317

Les.3757.1.S1_at

548

318

Les.376.1.S1_at

525

319

Les.3766.1.S1_at

304

320

Les.3774.1.S1_at

379

321

Les.3775.1.S1_at

521

322

Les.3779.1.S1_at

444

Solyc11g011030.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:40858354088919 functional_description:"Pto-responsive gene 1 protein (AHRD V1 ***- Q9M723_SOLLC); contains Interpro domain(s) IPR010399 Tify " *******

551

3E-57

*******

*******

******* Solyc12g095860.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6331641963319859 functional_description:"Cell division protein kinase 2 (AHRD V1 **** B5X1T4_SALSA); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc09g082340.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6349075663493632 functional_description:"Vicilin-like protein (Fragment) (AHRD V1 **-- Q9SEW4_9ROSI); contains Interpro domain(s) IPR014710 RmlC-like jelly roll fold " Solyc03g006490.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:10746951077139 functional_description:"Aluminum-induced protein-like (AHRD V1 ***- Q9FG81_ARATH)" Solyc02g063150.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:2980218829802925 functional_description:"Ribulose bisphosphate carboxylase small chain (AHRD V1 ***Q84QE5_TOBAC); contains Interpro domain(s) IPR000894 Ribulose bisphosphate carboxylase, small chain " Solyc01g095140.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7828360478284178 functional_description:"Late embryogenesis abundant protein (Fragment) (AHRD V1 **-B7TGG5_PINSY); contains Interpro domain(s) IPR013990 Water Stress and Hypersensitive response " Solyc09g075820.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6293174162937215 functional_description:"Solute carrier family 2, facilitated glucose transporter member 3 (AHRD V1 ***GTR3_CANFA); contains Interpro domain(s) IPR003663 Sugar/inositol transporter " Solyc05g056050.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6459828164600161 functional_description:"Chlorophyll a-b binding protein 6A, chloroplastic (AHRD V1 ***- CB11_SOLLC); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc02g082930.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4113243841133540 functional_description:"Endochitinase (Chitinase) (AHRD V1 **** Q43184_SOLTU); contains Interpro domain(s) IPR016283 Glycoside hydrolase, family 19 IPR000726 Glycoside hydrolase, family 19, catalytic "

*******

*******

224

4E-19

279

6E-26

696

7E-74

713

7E-76

528

8E-55

206

2E-17

802

3E-86

688

4E-73


Les.3792.1.S1_s_at

403

324

Les.3807.1.S1_at

497

325

Les.3819.1.S1_at

474

326

Les.3828.1.S1_at

384

327

Les.392.1.S1_at

541

328

Les.3932.1.S1_at

356

329

Les.396.2.A1_at

133

330

Les.3962.1.A1_at

331

331

Les.3964.1.S1_at

338

332

Les.397.1.S1_at

245

333

Les.3979.1.S1_at

476

Solyc07g043460.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5457119654573054 functional_description:"Cytochrome P450 (AHRD V1 ***- A9ZT56_COPJA); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc08g078950.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5977636259780516 functional_description:"Nitrate transporter (AHRD V1 **** Q852P7_TOBAC); contains Interpro domain(s) IPR000109 TGF-beta receptor, type I/II extracellular region " Solyc03g034100.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E0IEG gene_region:1007176510073365 functional_description:"Plant-specific domain TIGR01568 family protein (AHRD V1 *--B6U561_MAIZE); contains Interpro domain(s) IPR006458 Protein of unknown function DUF623, plant " Solyc11g011330.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E0IEG gene_region:43753924377544 functional_description:"Cinnamyl alcohol dehydrogenase (AHRD V1 **** D1FWZ8_SOYBN); contains Interpro domain(s) IPR002085 Alcohol dehydrogenase superfamily, zinc-containing " Solyc06g073090.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4141955741422920 functional_description:"Ribosomal subunit interface protein (AHRD V1 **-- Q2JIS4_SYNJB); contains Interpro domain(s) IPR003489 Ribosomal protein S30Ae/sigma 54 modulation protein " Solyc10g085550.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6399477563999383 functional_description:"Enolase (AHRD V1 ***C5J0G6_TOBAC); contains Interpro domain(s) IPR000941 Enolase " ******* Solyc09g066010.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:5988341859884888 functional_description:"WRKY transcription factor 25 (AHRD V1 ***- C9DI14_9ROSI); contains Interpro domain(s) IPR003657 DNA-binding WRKY " Solyc12g096350.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6365474163656107 functional_description:"WRKY transcription factor 11 (AHRD V1 ***- D7MB53_ARALY); contains Interpro domain(s) IPR003657 DNA-binding WRKY " Solyc06g068220.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3865165938657868 functional_description:"Hydrolase alpha/beta fold family protein (AHRD V1 ***- D7KJH6_ARALY); contains Interpro domain(s) IPR000639 Epoxide hydrolase-like " Solyc12g044880.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4568635845692372 functional_description:"Beta-galactosidase

431

2E-43

480

7E-49

382

1E-37

629

2E-66

481

6E-49

601

3E-63

*******

*******

227

7E-20

610

3E-64

381

9E-38

297

1E-27


334

Les.3980.1.S1_at

555

335

Les.3981.1.S1_at

549

336

Les.3985.1.S1_at

542

337

Les.3991.1.S1_at

523

338

Les.3998.1.S1_at

489

339

Les.4.1.S1_at

461

340

Les.4008.1.S1_a_at

36

341

Les.4008.2.S1_at

205

342

Les.4021.2.S1_at

207

343

Les.4022.1.S1_at

446

344

Les.4026.1.S1_at

510

(AHRD V1 ***- Q546T5_SOLLC); contains Interpro domain(s) IPR001944 Glycoside hydrolase, family 35 " Solyc01g006540.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:11139391123703 functional_description:"Lipoxygenase (AHRD V1 **** Q96573_SOLLC); contains Interpro domain(s) IPR001246 Lipoxygenase, plant " Solyc10g085230.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6382342663824995 functional_description:"UDP-glucosyltransferase (AHRD V1 **** C0LNQ9_MAIZE); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " ******* Solyc01g104950.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8503181485035555 functional_description:"Alpha-Larabinofuranosidase/beta- D-xylosidase (AHRD V1 **** D9D7L0_MALDO); contains Interpro domain(s) IPR001764 Glycoside hydrolase, family 3, N-terminal " Solyc01g056780.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:4944505749446052 functional_description:"50S ribosomal protein L34 (AHRD V1 *-*- D7KDQ0_ARALY); contains Interpro domain(s) IPR000271 Ribosomal protein L34 " Solyc12g006850.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:12596081266170 functional_description:"Potassium channel (AHRD V1 ***- Q9LEG6_SOLLC); contains Interpro domain(s) IPR002110 Ankyrin " ******* Solyc07g052980.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5872644658727898 functional_description:"Xyloglucan endotransglucosylase/hydrolase 5 (AHRD V1 **** C0IRH8_MALDO); contains Interpro domain(s) IPR016455 Xyloglucan endotransglucosylase/hydrolase " Solyc06g074260.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H0E1IEG gene_region:4229769242304159 functional_description:"Genomic DNA chromosome 5 P1 clone MWD9 (AHRD V1 *-*Q9FMQ8_ARATH); contains Interpro domain(s) IPR007608 Protein of unknown function DUF584 " Solyc03g020050.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:69192896920057 functional_description:"Proteinase inhibitor II (AHRD V1 ***- B3F0C1_TOBAC); contains Interpro domain(s) IPR003465 Proteinase inhibitor I20, Pin2 " Solyc01g080010.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7165057571651891 functional_description:"Xylanase inhibitor (Fragment) (AHRD V1 **-- Q53IQ4_WHEAT); contains Interpro domain(s) IPR001461 Peptidase A1 "

817

7E-88

568

5E-59

*******

*******

662

6E-70

423

3E-42

619

4E-65

*******

*******

364

9E-36

323

5E-31

715

3E-76

822

2E-88


Les.4032.1.A1_at

118

*******

*******

*******

346

Les.4034.1.S1_at

152

*******

*******

347

Les.4035.1.S1_at

375

624

7E-66

348

Les.4038.1.S1_at

433

489

5E-50

349

Les.4041.1.S1_s_at

243

172

2E-13

350

Les.4045.1.S1_at

49

*******

*******

351

Les.4067.1.S1_at

444

777

2E-83

352

Les.4080.1.S1_at

491

*******

*******

353

Les.4085.1.S1_at

170

281

4E-26

354

Les.4089.1.S1_at

213

205

2E-17

355

Les.4093.1.S1_at

353

516

2E-53

356

Les.4099.1.S1_at

566

924

1E-100

357

Les.4102.1.S1_at

427

******* Solyc07g006180.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:10080731013094 functional_description:"Tetratricopeptide repeat protein 4 homolog (AHRD V1 *--- TTC4_DICDI); contains Interpro domain(s) IPR011990 Tetratricopeptide-like helical " Solyc08g068770.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5510755855108286 functional_description:"N-acetyltransferase (AHRD V1 ***- B6SUK9_MAIZE); contains Interpro domain(s) IPR000182 GCN5-related N-acetyltransferase " Solyc01g060300.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E0IEG gene_region:6287873962882396 functional_description:"MADS-box transcription factor (AHRD V1 *-*- Q9SEE0_PICAB); contains Interpro domain(s) IPR002100 Transcription factor, MADS-box " ******* Solyc12g006450.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:923159-928400 functional_description:"Aminotransferase-like protein (AHRD V1 ***- Q9LIE2_ARATH); contains Interpro domain(s) IPR005814 Aminotransferase class-III " ******* Solyc11g068960.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5061444850620875 functional_description:"Uncharacterized basic helix-loop-helix protein At1g64625 (AHRD V1 *--Y1462_ARATH); contains Interpro domain(s) IPR001092 Basic helix-loop-helix dimerisation region bHLH " Solyc06g068620.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:3892877838929243 functional_description:"Unknown Protein (AHRD V1)" Solyc02g067440.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3220339232206673 functional_description:"Cupin RmlC-type (AHRD V1 **-- B4F886_MAIZE); contains Interpro domain(s) IPR012864 Protein of unknown function DUF1637 " Solyc06g053620.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3294245132943686 functional_description:"Calcium-dependent protein kinase 2 (AHRD V1 **** B4FZS4_MAIZE); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc09g075420.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6262556362626419 functional_description:"Ethylene responsive transcription factor 2b (AHRD V1 *-*- C0J9I6_9ROSA); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding

687

5E-73


358

Les.4140.1.S1_at

444

359

Les.4149.2.S1_a_at

299

360

Les.4150.1.S1_at

478

361

Les.417.1.S1_at

410

362

Les.4222.1.S1_at

557

363

Les.4259.1.S1_at

465

364

Les.4264.1.A1_s_at

192

365

Les.4287.1.S1_at

527

366

Les.4300.3.S1_at

348

367

Les.4307.1.S1_at

539

IPR001711 Phospholipase C, phosphatidylinositol-specific, Y domain " Solyc03g093610.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4847717748477905 functional_description:"Ethylene responsive transcription factor 1b (AHRD V1 **** C0J9I8_9ROSA); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc01g111040.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8920989189212692 functional_description:"EF-Hand containing protein-like (AHRD V1 ***- Q9T0I9_ARATH); contains Interpro domain(s) IPR018248 EF hand " Solyc08g078700.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5963540559636272 functional_description:"Heat shock protein 22 (AHRD V1 ***- Q27JQ0_METAN); contains Interpro domain(s) IPR002068 Heat shock protein Hsp20 " Solyc04g078200.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6059739960597978 functional_description:"Gibberellin-regulated family protein (AHRD V1 **-- D7MT35_ARALY); contains Interpro domain(s) IPR003854 Gibberellin regulated protein " Solyc08g075550.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5688141056884120 functional_description:"Alternative oxidase (AHRD V1 **** Q84V46_SOLLC); contains Interpro domain(s) IPR002680 Alternative oxidase " Solyc10g007690.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:19506821952398 functional_description:"Chlorophyll a-b binding protein 8, chloroplastic (AHRD V1 ***- CB13_SOLLC); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc12g006450.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:923159-928400 functional_description:"Aminotransferase-like protein (AHRD V1 ***- Q9LIE2_ARATH); contains Interpro domain(s) IPR005814 Aminotransferase class-III " Solyc03g083730.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4721725247217857 functional_description:"Pectinesterase (AHRD V1 ***- C0PST8_PICSI); contains Interpro domain(s) IPR006501 Pectinesterase inhibitor " Solyc08g067030.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5314357353148054 functional_description:"Os01g0611000 protein (Fragment) (AHRD V1 ***- Q0JLB5_ORYSJ); contains Interpro domain(s) IPR006946 Protein of unknown function DUF642 " Solyc08g080670.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6105660361057355 functional_description:"Osmotin-like protein

414

2E-41

501

1E-51

565

9E-59

388

2E-38

888

4E-96

615

1E-64

248

2E-22

608

1E-63

598

6E-63

724

4E-77


368

Les.4312.2.S1_at

344

369

Les.4333.1.S1_at

438

370

Les.4339.1.S1_at

563

371

Les.4345.1.S1_at

532

372

Les.4345.2.A1_x_at

319

373

Les.4346.1.S1_at

569

374

Les.435.1.S1_at

448

375

Les.4362.1.A1_at

435

376

Les.4376.1.S1_at

457

(Fragment) (AHRD V1 **-- Q6TGR8_SOLTU); contains Interpro domain(s) IPR001938 Thaumatin, pathogenesisrelated " Solyc08g074480.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5574781655748211 functional_description:"Cortical cell-delineating protein (AHRD V1 **-- B6UGA2_MAIZE); contains Interpro domain(s) IPR013770 Plant lipid transfer protein and hydrophobic protein, helical " Solyc10g075110.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H0E1IEG gene_region:5815590058156508 functional_description:"Non-specific lipidtransfer protein (AHRD V1 ***- A7UGG9_SOLTU); contains Interpro domain(s) IPR000528 Plant lipid transfer protein/Par allergen " Solyc03g114830.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5875253358758410 functional_description:"MADS box transcription factor (AHRD V1 ***- Q9SBQ1_PETHY); contains Interpro domain(s) IPR002487 Transcription factor, K-box " Solyc02g070940.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3508015635080953 functional_description:"Chlorophyll a/b binding protein (AHRD V1 **** Q41422_SOLTU); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc02g071030.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3510293735103734 functional_description:"Chlorophyll a/b binding protein (AHRD V1 **** Q41422_SOLTU); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc12g008840.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:21849712191441 functional_description:"Beta-galactosidase (AHRD V1 ***- O81100_SOLLC); contains Interpro domain(s) IPR001944 Glycoside hydrolase, family 35 " Solyc05g050130.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:5925475959256287 functional_description:"Acidic chitinase (AHRD V1 **-- Q71HN4_FICAW); contains Interpro domain(s) IPR001223 Glycoside hydrolase, family 18, catalytic domain " Solyc05g012020.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:52170335230668 functional_description:"MADS-box transcription factor MADS-MC (AHRD V1 *-** Q8S4L5_SOLLC); contains Interpro domain(s) IPR002487 Transcription factor, K-box " Solyc04g072240.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5683568556837473 functional_description:"Oxidoreductase family protein (AHRD V1 ***- D7LXC3_ARALY); contains

357

6E-35

376

6E-37

432

3E-43

643

7E-78

567

3E-59

520

2E-53

690

2E-73

743

2E-79

731

4E-78

Table S1 List of differentially expressed genes in rin mutant. Interpro domain(s) IPR016040 NAD(P)-binding domain " 377

Les.4386.1.S1_at

537

378

Les.441.1.S1_s_at

372

379

Les.4412.1.A1_at

131

380

Les.4437.1.S1_at

272

381

Les.4439.1.S1_at

544

382

Les.4442.1.S1_s_at

537

383

Les.4443.1.A1_s_at

105

384

Les.4445.1.S1_at

543

385

Les.4449.1.S1_s_at

445

386

Les.4450.1.S1_at

305

387

Les.4455.1.S1_at

484

******* Solyc12g100250.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6537408965375228 functional_description:"Fatty acid desaturase (AHRD V1 ***- B3SP99_CAPAN); contains Interpro domain(s) IPR005804 Fatty acid desaturase, type 1 " Solyc11g072110.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5245467552456389 functional_description:"1AMINOCYCLOPROPANE-1- CARBOXYLATE OXIDASE-like protein (AHRD V1 **-Q94CL5_ARATH); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc09g007560.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:11579861159211 functional_description:"50S ribosomal protein L5 (AHRD V1 ***- B5TV71_CAMSI); contains Interpro domain(s) IPR002132 Ribosomal protein L5 " Solyc01g079110.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7068124370681653 functional_description:"Histone H3 (AHRD V1 ***- D8L9K7_WHEAT); contains Interpro domain(s) IPR000164 Histone H3 " Solyc06g074790.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4271478142715209 functional_description:"Histone H2B (AHRD V1 ***- Q2XTD8_SOLTU); contains Interpro domain(s) IPR000558 Histone H2B " Solyc02g089160.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4562231245624870 functional_description:"Cytochrome P450 (AHRD V1 ***- B9N6N1_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc10g047030.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:3470240534706544 functional_description:"Beta-xylosidase 4 (AHRD V1 **** D7MRV5_ARALY); contains Interpro domain(s) IPR001764 Glycoside hydrolase, family 3, Nterminal " Solyc01g008710.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:27551382757943 functional_description:"Mannan endo-1 4-betamannosidase (AHRD V1 ***- D2S259_HALTV); contains Interpro domain(s) IPR018087 Glycoside hydrolase, family 5, conserved site IPR013781 Glycoside hydrolase, subgroup, catalytic core " ******* Solyc11g011990.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:49379494942634 functional_description:"Alternative oxidase (AHRD V1 ***- Q9FEC9_SOLLC); contains Interpro domain(s) IPR002680 Alternative oxidase "

*******

*******

539

5E-56

236

6E-21

436

4E-44

533

6E-55

438

6E-44

182

1E-14

923

1E-100

588

2E-61

*******

*******

875

1E-94


Les.4460.1.S1_at

347

389

Les.4463.1.S1_s_at

316

390

Les.4487.1.S1_at

524

391

Les.4492.2.S1_at

290

392

Les.4492.3.S1_at

219

393

Les.450.1.S1_at

379

394

Les.4501.1.S1_at

401

395

Les.4520.1.S1_at

310

396

Les.4522.1.S1_at

419

397

Les.4529.1.S1_at

555

398

Les.4530.1.S1_at

589

Solyc01g097240.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7992353679924077 functional_description:"Pathogenesis-related protein 4B (Fragment) (AHRD V1 **-Q6LBM4_TOBAC); contains Interpro domain(s) IPR018226 Barwin, conserved site IPR001153 Barwin " Solyc10g080210.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6088250060889135 functional_description:"Polygalacturonase A (AHRD V1 **** Q9M6S2_ACTCH); contains Interpro domain(s) IPR000743 Glycoside hydrolase, family 28 " ******* Solyc01g105050.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8509388785094755 functional_description:"Chlorophyll a-b binding protein, chloroplastic (AHRD V1 **** CB12_PETHY); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc01g105050.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8509388785094755 functional_description:"Chlorophyll a-b binding protein, chloroplastic (AHRD V1 **** CB12_PETHY); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc09g061280.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:5412937454131654 functional_description:"Cyclin dependent kinase inhibitor (AHRD V1 **** Q5PXG5_EUPES); contains Interpro domain(s) IPR016701 Cyclin-dependent kinase inhibitor, plant " Solyc09g011590.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:48674184868723 functional_description:"Glutathione S-transferaselike protein (AHRD V1 **** A8DUB0_SOLLC); contains Interpro domain(s) IPR004046 Glutathione S-transferase, C-terminal " Solyc02g065770.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3148983431492931 functional_description:"COBRA-like protein 4 (AHRD V1 ***- B6SST3_MAIZE); contains Interpro domain(s) IPR017391 COBRA-like " Solyc11g066270.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4908409449086198 functional_description:"Xyloglucan endotransglucosylase/hydrolase 9 (AHRD V1 ***C0IRI2_MALDO); contains Interpro domain(s) IPR016455 Xyloglucan endotransglucosylase/hydrolase " Solyc02g091920.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4771466247716016 functional_description:"Xyloglucan endotransglucosylase/hydrolase 2 (AHRD V1 **** Q2MK81_9ROSA); contains Interpro domain(s) IPR016455 Xyloglucan endotransglucosylase/hydrolase " Solyc07g055990.1.1 genomic_reference:SL2.31ch07

637

2E-67

446

3E-45

*******

*******

530

5E-55

312

9E-30

251

1E-22

549

4E-57

286

9E-27

602

3E-63

875

1E-94

673

4E-71


399

Les.4589.1.S1_at

492

400

Les.4603.1.S1_at

383

401

Les.4605.1.S1_at

503

402

Les.4609.1.S1_at

437

403

Les.4615.1.S1_at

489

404

Les.4616.1.S1_at

474

405

Les.4617.1.S1_at

569

406

Les.4649.1.S1_at

224

evidence_code:10F0H1E1IEG gene_region:6121923361220965 functional_description:"Xyloglucan endotransglucosylase/hydrolase 7 (AHRD V1 **** C0IRG6_ACTDE); contains Interpro domain(s) IPR016455 Xyloglucan endotransglucosylase/hydrolase " Solyc03g034370.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H0E1IEG gene_region:1047590710476098 functional_description:"Unknown Protein (AHRD V1)" Solyc01g073970.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7056457370564983 functional_description:"Histone H3 (AHRD V1 ***- D8L9K7_WHEAT); contains Interpro domain(s) IPR000164 Histone H3 " Solyc06g030470.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:1543636815438085 functional_description:"Auxin-regulated protein (AHRD V1 ***- Q945F5_SOLLC); contains Interpro domain(s) IPR010369 Protein of unknown function DUF966 " Solyc00g127870.1.1 genomic_reference:SL2.31ch00 evidence_code:10F0H1E0IEG gene_region:1672469416727659 functional_description:"Phosphatidylinositol Nacetylglucosaminyltransferase subunit P (AHRD V1 ***B6TUG3_MAIZE); contains Interpro domain(s) IPR013717 PIG-P " Solyc07g055050.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6050744760511311 functional_description:"ATP synthase I-like protein (AHRD V1 **-- A8HNA8_CHLRE); contains Interpro domain(s) IPR008413 ATPase, F0 complex, subunit I, bacillus-type " Solyc09g011810.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:50913165093654 functional_description:"Fructose-1 6bisphosphatase class 1 (AHRD V1 **** D0MHZ8_RHOM4); contains Interpro domain(s) IPR000146 Fructose-1,6-bisphosphatase " Solyc07g005390.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:296514-301290 functional_description:"Aldehyde dehydrogenase (AHRD V1 **** A7GLM2_BACCN); contains Interpro domain(s) IPR015590 Aldehyde dehydrogenase " *******

407

Les.4649.1.S1_s_at

481

408

Les.467.2.A1_at

121

409

Les.4678.1.S1_at

410

410

Les.4681.1.S1_at

481

322

1E-30

430

1E-47

203

9E-17

379

3E-37

508

4E-52

531

7E-55

670

8E-71

*******

*******

*******

*******

*******

******* Solyc10g086760.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6480685564808380 functional_description:"Tubulin beta chain (AHRD V1 ***- B9HP96_POPTR); contains Interpro domain(s) IPR002453 Beta tubulin " Solyc01g074030.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:70604189-

*******

*******

403

4E-40

717

2E-76


411

Les.4693.1.S1_at

280

412

Les.4701.1.S1_at

513

413

Les.4703.1.S1_at

450

414

Les.4705.1.S1_at

477

415

Les.4709.1.S1_at

374

416

Les.471.1.S1_at

512

417

Les.4721.1.S1_at

498

418

Les.4724.1.S1_at

463

419

Les.4727.1.S1_at

507

70610830 functional_description:"Beta-glucosidase 01 (AHRD V1 ***- B5M9E4_SOLLC); contains Interpro domain(s) IPR013781 Glycoside hydrolase, subgroup, catalytic core " Solyc09g007010.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:687712-688191 functional_description:"Pathogenesis related protein PR-1 (AHRD V1 **-- Q9SC15_SOLTU); contains Interpro domain(s) IPR002413 Ves allergen " Solyc09g097960.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6719101767192457 functional_description:"Aldo/keto reductase family protein (AHRD V1 **-- D7KWQ9_ARALY); contains Interpro domain(s) IPR001395 Aldo/keto reductase " Solyc10g080940.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6145261861455201 functional_description:"Tubulin beta chain (AHRD V1 ***- B9HNJ2_POPTR); contains Interpro domain(s) IPR002453 Beta tubulin " Solyc02g079930.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3889553938898763 functional_description:"Phosphosulfolactate synthase (AHRD V1 ***- Q1ASZ8_RUBXD); contains Interpro domain(s) IPR003830 (2R)-phospho-3sulpholactate synthase, ComA " Solyc11g067160.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4997734949981087 functional_description:"Aldo/keto reductase family protein (AHRD V1 ***- D7LJ14_ARALY); contains Interpro domain(s) IPR001395 Aldo/keto reductase " Solyc02g068280.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3283944632843357 functional_description:"Subtilisin-like serine protease (AHRD V1 **-* C3VDI0_CARPA); contains Interpro domain(s) IPR015500 Peptidase S8, subtilisinrelated " Solyc06g069580.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3972301039727252 functional_description:"Heparanase-like protein 2 (AHRD V1 **** B6U6D3_MAIZE); contains Interpro domain(s) IPR005199 Glycoside hydrolase family 79, Nterminal " Solyc03g007920.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:24295002433781 functional_description:"Glutamine cyclotransferase-like (AHRD V1 **** Q2V9A5_SOLTU); contains Interpro domain(s) IPR007788 Glutamine cyclotransferase " Solyc05g005460.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:341827-347035 functional_description:"Nucleoredoxin 2 (AHRD V1 *--A8I9J4_CHLRE); contains Interpro domain(s) IPR000866 Alkyl hydroperoxide reductase/ Thiol specific antioxidant/

179

2E-14

738

9E-79

421

4E-42

404

4E-40

618

3E-65

503

2E-51

657

2E-69

657

2E-69

504

1E-51

Table S1 List of differentially expressed genes in rin mutant. Mal allergen " 420

Les.4752.1.S1_at

440

421

Les.4766.1.S1_at

359

422

Les.477.1.S1_at

531

423

Les.4773.1.S1_at

441

424

Les.4794.1.S1_at

483

425

Les.4798.1.S1_at

511

426

Les.4803.1.S1_at

512

427

Les.4808.1.S1_at

544

428

Les.4829.1.S1_at

263

429

Les.4834.1.S1_at

518

430

Les.4835.1.S1_at

525

Solyc09g011030.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:43697524374017 functional_description:"Hsp70 nucleotide exchange factor fes1 (AHRD V1 *-*- C8V0S6_EMENI); contains Interpro domain(s) IPR011989 Armadillo-like helical " Solyc02g083880.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4171550541715991 functional_description:"Gibberellin-regulated protein 2 (AHRD V1 *--- B6SKV6_MAIZE); contains Interpro domain(s) IPR003854 Gibberellin regulated protein " Solyc08g082120.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6217147862172800 functional_description:"Methanol inducible protein (AHRD V1 ***- D1MAX5_NICBE)" Solyc04g078750.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6100683261008136 functional_description:"Harpin-induced protein (AHRD V1 ***- B6TDG9_MAIZE); contains Interpro domain(s) IPR010847 Harpin-induced 1 " ******* Solyc01g008550.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:26469292650181 functional_description:"Cinnamoyl CoA reductase-like protein (AHRD V1 ***- B9HNY0_POPTR); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc02g089630.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4595942845961662 functional_description:"Proline dehydrogenase (AHRD V1 **** A1E289_ACTDE); contains Interpro domain(s) IPR015659 Proline oxidase " Solyc05g026240.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:4018085840182033 functional_description:"Leucine-rich repeat receptor protein kinase EXS (AHRD V1 *--* EXS_ARATH); contains Interpro domain(s) IPR013210 Leucine-rich repeat, N-terminal " Solyc12g006380.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:889953-892184 functional_description:"1-aminocyclopropane-1carboxylate oxidase-like protein (AHRD V1 **-* Q9LTH7_ARATH); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc04g071140.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5566300755667366 functional_description:"Decarboxylase family protein (AHRD V1 ***- B1ILJ6_CLOBK); contains Interpro domain(s) IPR002129 Pyridoxal phosphatedependent decarboxylase " Solyc06g068950.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:39165953-

423

2E-42

503

7E-52

867

1E-93

312

2E-29

*******

*******

647

3E-68

455

6E-46

899

2E-97

468

8E-48

503

2E-51

646

4E-68


431

Les.4849.1.S1_at

390

432

Les.4855.1.S1_at

496

433

Les.4865.1.S1_at

544

434

Les.4876.1.S1_at

411

435

Les.4889.1.S1_at

465

436

Les.4890.1.S1_at

563

437

Les.4920.1.S1_at

434

438

Les.4923.1.S1_at

511

439

Les.4924.1.S1_at

460

39169654 functional_description:"Phosphoethanolamine Nmethyltransferase (AHRD V1 **** Q9AXH3_SOLLC); contains Interpro domain(s) IPR013216 Methyltransferase type 11 " Solyc03g025410.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:72098437215083 functional_description:"Dehydrogenase/reductase SDR family member 13 (AHRD V1 ***- DHR13_BOVIN); contains Interpro domain(s) IPR002347 Glucose/ribitol dehydrogenase " Solyc06g071050.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4004421940045774 functional_description:"Spfh domain / band 7 family protein (AHRD V1 **-- B4AS86_FRANO); contains Interpro domain(s) IPR001107 Band 7 protein " Solyc12g095850.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6330545963315472 functional_description:"Tryptophanyl-tRNA synthetase (AHRD V1 ***- B4AZK3_9CHRO); contains Interpro domain(s) IPR002306 Tryptophanyl-tRNA synthetase, class Ib " Solyc11g069700.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:5139113051392793 functional_description:"Elongation factor 1-alpha (AHRD V1 ***- P93769_TOBAC); contains Interpro domain(s) IPR004539 Translation elongation factor EF1A, eukaryotic and archaeal " Solyc11g068800.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5050339750508088 functional_description:"Transcription factor (E2F) (AHRD V1 ***- Q9FNS0_CHERU); contains Interpro domain(s) IPR015633 E2F Family " Solyc03g083090.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4645438446465031 functional_description:"Glycogen synthase (AHRD V1 ***- D5MWN9_BACSU); contains Interpro domain(s) IPR011835 Glycogen/starch synthases, ADPglucose type " Solyc04g079310.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6141156161416408 functional_description:"RNA Binding Protein 47 (AHRD V1 **-* Q9LEB3_NICPL); contains Interpro domain(s) IPR012677 Nucleotide-binding, alpha-beta plait " Solyc10g005080.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:76066-79178 functional_description:"Late elongated hypocotyl and circadian clock associated-1-like protein 1 (AHRD V1 **-C0SNP1_SOYBN)" Solyc09g090470.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6532961165336150 functional_description:"Peptide transporter (AHRD V1 **-* A6YJX4_9MAGN); contains Interpro domain(s) IPR000109 TGF-beta receptor, type I/II

599

6E-63

580

2E-60

352

5E-34

190

2E-15

158

1E-11

654

6E-69

341

7E-33

488

8E-50

241

3E-21

Table S1 List of differentially expressed genes in rin mutant. extracellular region " 440

Les.4929.1.S1_at

569

441

Les.4953.1.S1_at

562

442

Les.4957.1.S1_at

460

443

Les.4959.1.S1_at

485

444

Les.4964.1.S1_at

475

445

Les.4965.1.S1_at

332

446

Les.4974.1.S1_at

282

447

Les.4979.1.S1_at

469

448

Les.4994.1.S1_at

430

449

Les.4999.1.S1_at

512

450

Les.5010.1.S1_at

475

Solyc02g087840.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4467561044676979 functional_description:"Homeobox-leucine zipper-like protein (AHRD V1 *-*- Q3HRT1_PICGL); contains Interpro domain(s) IPR001356 Homeobox " Solyc06g075650.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4340712043408047 functional_description:"Aquaporin (AHRD V1 ***- D6BRE1_9ROSI); contains Interpro domain(s) IPR012269 Aquaporin " Solyc09g007940.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:14400181443977 functional_description:"Adenosine kinase (AHRD V1 **** D2D2Z6_GOSHI); contains Interpro domain(s) IPR001805 Adenosine kinase " Solyc10g007110.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:15082891511165 functional_description:"Tyrosine aminotransferase (AHRD V1 **** Q8GUE9_SOLSC); contains Interpro domain(s) IPR005958 Tyrosine/nicotianamine aminotransferase " Solyc04g055160.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5292930852932259 functional_description:"cDNA clone J033025P19 full insert sequence (AHRD V1 ***- B7ERC6_ORYSJ)" ******* Solyc09g011140.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:45012084503800 functional_description:"Tropinone reductase I (AHRD V1 **-- B2L2W8_9SOLA); contains Interpro domain(s) IPR002347 Glucose/ribitol dehydrogenase " Solyc06g068440.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3879461538796908 functional_description:"Cinnamoyl-CoA reductase (AHRD V1 **** Q4U1I5_SOLLC); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc05g050580.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:5988418559888239 functional_description:"E3 ubiquitin-protein ligase sina (AHRD V1 **-* B0WR23_CULQU); contains Interpro domain(s) IPR004162 Seven in absentia protein " Solyc09g007520.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:10931511096675 functional_description:"Peroxidase (AHRD V1 **** C1KA92_POPTR); contains Interpro domain(s) IPR000823 Plant peroxidase " Solyc01g090200.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7558559775617298 functional_description:"Glycyl-tRNA synthetase beta subunit (AHRD V1 ***- D2PQC6_KRIFD); contains Interpro domain(s) IPR002311 Glycyl-tRNA synthetase, class IIc, beta subunit, N-terminal "

670

8E-71

764

1E-81

611

4E-64

712

8E-76

698

3E-74

*******

*******

469

6E-48

544

2E-56

245

9E-22

716

3E-76

639

1E-81


Les.5015.1.S1_at

545

452

Les.5017.1.A1_at

529

453

Les.5018.1.S1_at

518

454

Les.5019.1.S1_at

522

455

Les.5039.1.S1_at

449

456

Les.5051.1.S1_at

246

457

Les.5056.1.S1_x_at

546

458

Les.506.1.A1_at

319

459

Les.5060.1.S1_at

532

460

Les.5064.1.S1_at

480

461

Les.5072.1.S1_at

495

Solyc11g011920.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:48487904855188 functional_description:"Glutamate decarboxylase (AHRD V1 ***- Q8LKR4_TOBAC); contains Interpro domain(s) IPR010107 Glutamate decarboxylase " Solyc11g073120.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E0IEG gene_region:5329639153297625 functional_description:"MYB transcription factor (AHRD V1 *-*- Q56UT4_ORYSJ); contains Interpro domain(s) IPR015495 Myb transcription factor " Solyc05g056270.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6476455764771563 functional_description:"Isocitrate lyase (AHRD V1 *-*- Q2TWG5_ASPOR); contains Interpro domain(s) IPR000918 Isocitrate lyase and phosphorylmutase " Solyc01g098700.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8087852580889284 functional_description:"Branched-chain amino acid aminotransferase-like protein (AHRD V1 ***Q84L60_CICAR); contains Interpro domain(s) IPR001544 Aminotransferase, class IV " Solyc08g005420.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:313265-315876 functional_description:"WD repeat-containing protein 5 homolog (AHRD V1 *--- WDR5_DICDI); contains Interpro domain(s) IPR017986 WD40 repeat, region " Solyc05g008220.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:26148092616449 functional_description:"Unknown Protein (AHRD V1)" Solyc11g071760.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:5222461752225213 functional_description:"Calmodulin-like protein (AHRD V1 ***- Q0VJ70_DATME); contains Interpro domain(s) IPR018248 EF hand " Solyc07g007260.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:19925041993403 functional_description:"Metallocarboxypeptidase inhibitor (AHRD V1 ***- MCPI_SOLLC); contains Interpro domain(s) IPR004231 Proteinase inhibitor I37, carboxypeptidase A " Solyc08g081490.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6169674161699680 functional_description:"Mitogen-activated protein kinase (AHRD V1 **** Q8LT16_SOLTU); contains Interpro domain(s) IPR008351 JNK MAP kinase " Solyc01g094790.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7795745477959857 functional_description:"Cysteine synthase (AHRD V1 ***- Q9FS29_SOLTU); contains Interpro domain(s) IPR005859 Cysteine synthase A " Solyc02g068270.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:32825974-

602

6E-63

362

4E-35

547

1E-56

573

1E-59

810

3E-87

319

1E-30

758

5E-81

431

1E-43

560

4E-58

592

6E-62

174

2E-13


462

Les.5080.1.S1_at

422

463

Les.5092.1.S1_at

411

464

Les.5096.1.S1_at

538

465

Les.5102.1.S1_at

416

466

Les.5113.1.S1_at

450

467

Les.5120.1.S1_at

550

468

Les.5124.1.S1_at

405

469

Les.5130.1.S1_at

504

470

Les.5139.1.S1_at

468

471

Les.514.1.S1_at

520

32828609 functional_description:"Unknown Protein (AHRD V1)" Solyc11g010370.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:34479733449022 functional_description:"At4g40080-like protein (Fragment) (AHRD V1 ***- B3SK88_ARALP); contains Interpro domain(s) IPR013809 Epsin-like, N-terminal " Solyc10g038080.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:1937458919383493 functional_description:"Shikimate dehydrogenase (AHRD V1 ***- B6TSW1_MAIZE); contains Interpro domain(s) IPR001381 Dehydroquinase class I " Solyc06g073080.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E0IEG gene_region:4140982341412466 functional_description:"Flavonol synthase/flavanone 3-hydroxylase (AHRD V1 **-* FLS_PETHY); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc07g055280.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:6069537860698847 functional_description:"WRKY transcription factor 5 (AHRD V1 ***- A7UGD2_SOLTU); contains Interpro domain(s) IPR003657 DNA-binding WRKY " Solyc11g071280.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:5189265851896145 functional_description:"Branched-chain amino acid aminotransferase like protein (AHRD V1 **** Q0WW83_ARATH); contains Interpro domain(s) IPR001544 Aminotransferase, class IV " Solyc10g006900.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:13351521338590 functional_description:"Protochlorophyllide reductase (AHRD V1 ***- Q8LAV9_ARATH); contains Interpro domain(s) IPR005979 Light-dependent protochlorophyllide reductase " Solyc03g120850.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6315113863155284 functional_description:"chaperonin (AHRD V1 ***- B2IXD2_NOSP7); contains Interpro domain(s) IPR001844 Chaperonin Cpn60 " Solyc11g013330.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:63209336322474 functional_description:"F2E2.8 (AHRD V1 ***Q9LM58_ARATH)" Solyc07g062490.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6243609462436987 functional_description:"S-locus-specific glycoprotein (AHRD V1 **-- SLSG0_BRAOA); contains Interpro domain(s) IPR001480 Curculin-like (mannosebinding) lectin " Solyc07g042440.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5290558352907763 functional_description:"Alkyl hydroperoxide reductase/Thiol specific antioxidant family protein (AHRD

693

9E-74

677

6E-72

614

2E-64

429

4E-43

468

1E-47

642

1E-67

210

9E-18

653

6E-69

549

6E-57

389

3E-38


472

Les.5146.1.S1_at

398

473

Les.5158.1.S1_at

530

474

Les.5160.1.S1_at

501

475

Les.5167.1.S1_at

457

476

Les.5168.1.S1_at

513

477

Les.5173.1.S1_at

444

478

Les.5177.1.S1_at

437

479

Les.5188.1.S1_at

467

480

Les.5190.1.S1_at

461

481

Les.5196.1.S1_at

391

V1 **-- B0C2Q1_ACAM1); contains Interpro domain(s) IPR000866 Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen " Solyc01g110560.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8897440588974860 functional_description:"Auxin responsive SAUR protein (AHRD V1 *-*- Q1SN26_MEDTR); contains Interpro domain(s) IPR003676 Auxin responsive SAUR protein " Solyc02g084410.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4210379442104557 functional_description:"Glyoxalase (AHRD V1 ***- B4ERW1_WHEAT); contains Interpro domain(s) IPR004360 Glyoxalase/bleomycin resistance protein/dioxygenase " Solyc12g098960.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6464618864648764 functional_description:"Receptor-like protein kinase (AHRD V1 ***- Q9LYS5_ARATH); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc05g052950.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6226799962273266 functional_description:"Regulator of chromosome condensation RCC1 domain-containing protein (AHRD V1 *--- B9PXR3_TOXGO); contains Interpro domain(s) IPR009091 Regulator of chromosome condensation/beta-lactamase-inhibitor protein II " Solyc11g072380.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5264378652647057 functional_description:"Vicilin-like protein (Fragment) (AHRD V1 **-- Q9SEW4_9ROSI); contains Interpro domain(s) IPR011051 Cupin, RmlC-type " ******* Solyc02g064830.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3053436430536427 functional_description:"Indole-3-acetic acidamido synthetase GH3.8 (AHRD V1 **** B6U4E2_MAIZE); contains Interpro domain(s) IPR004993 GH3 auxin-responsive promoter " Solyc04g008840.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:24584662461537 functional_description:"ABI3-interacting protein 2 (Fragment) (AHRD V1 *-*- A7Y4K9_PINSY); contains Interpro domain(s) IPR012474 Frigida-like " Solyc02g085340.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4283508042836909 functional_description:"GRAS family transcription factor (AHRD V1 **-* B9MXP6_POPTR); contains Interpro domain(s) IPR005202 GRAS transcription factor " Solyc06g073110.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4142645941433062 functional_description:"Legume lectin beta

447

3E-45

649

2E-68

592

7E-62

174

2E-13

384

1E-37

*******

*******

756

5E-81

542

4E-56

668

9E-71

379

2E-37


482

Les.5198.1.S1_at

536

483

Les.5201.1.S1_at

375

484

Les.5202.1.S1_at

458

485

Les.5208.1.S1_at

410

486

Les.5216.1.S1_at

370

487

Les.5226.1.S1_at

299

488

Les.5229.1.S1_at

515

489

Les.5231.1.S1_at

542

490

Les.5233.1.S1_at

527

491

Les.5241.1.S1_at

541

domain (AHRD V1 *-*- A2Q3C0_MEDTR); contains Interpro domain(s) IPR010341 Protein of unknown function DUF936, plant " Solyc02g076680.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3640270236404964 functional_description:"Unknown Protein (AHRD V1); contains Interpro domain(s) IPR007789 Protein of unknown function DUF688 " Solyc11g066320.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4912840649130013 functional_description:"Exostosin-like glycosyltransferase (AHRD V1 **-- A8I7L6_CHLRE); contains Interpro domain(s) IPR004263 Exostosin-like " Solyc01g008290.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:23968252404598 functional_description:"Dihydroorotate dehydrogenase (AHRD V1 ***- B6U892_MAIZE); contains Interpro domain(s) IPR005719 Dihydroorotate dehydrogenase, class 2 " Solyc06g071280.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4024355540246220 functional_description:"Enhanced disease susceptibility 1 (Fragment) (AHRD V1 **-B2BDU7_ARALY); contains Interpro domain(s) IPR002921 Lipase, class 3 " Solyc07g006780.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:16245761635648 functional_description:"Glycerol kinase (AHRD V1 ***- GLPK_PYRFU); contains Interpro domain(s) IPR006003 Carbohydrate kinase, FGGY-related " Solyc12g014610.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:56112305617240 functional_description:"WRKY transcription factor 78 (AHRD V1 ***- Q5HZ67_ORYSA); contains Interpro domain(s) IPR003657 DNA-binding WRKY " Solyc06g008620.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:25174722519454 functional_description:"Protein tolB (AHRD V1 **- D3SF14_THISK); contains Interpro domain(s) IPR011042 Six-bladed beta-propeller, TolB-like " Solyc08g013730.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:30926623095742 functional_description:"Aquaporin (AHRD V1 ***- B3GK86_ARATH); contains Interpro domain(s) IPR000425 Major intrinsic protein " Solyc03g123620.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6447305164475638 functional_description:"Pectinesterase (AHRD V1 ***- B9GXZ7_POPTR); contains Interpro domain(s) IPR000070 Pectinesterase, catalytic " Solyc02g068370.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3290159832906092 functional_description:"Receptor-like kinase (AHRD V1 *-*- A7VM65_9VIRI); contains Interpro

340

3E-33

413

2E-41

465

3E-47

576

3E-60

388

2E-38

277

1E-25

704

8E-75

417

2E-41

713

7E-76

453

1E-45

Table S1 List of differentially expressed genes in rin mutant. domain(s) IPR002290 Serine/threonine protein kinase " 492

Les.5245.1.S1_at

529

493

Les.526.1.A1_at

120

494

Les.5279.1.S1_at

465

495

Les.5285.1.S1_at

466

496

Les.5287.1.S1_at

433

497

Les.5293.1.S1_at

468

498

Les.5309.1.S1_at

508

499

Les.5313.1.S1_at

451

500

Les.5322.1.S1_at

518

501

Les.5354.1.S1_at

344

502

Les.5355.1.S1_at

488

Solyc08g066360.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5215633452162368 functional_description:"Malic enzyme (AHRD V1 ***- B9RKI6_RICCO); contains Interpro domain(s) IPR012302 Malic enzyme, NAD-binding " Solyc11g007910.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:21341462140883 functional_description:"Neuralized (Fragment) (AHRD V1 *--- Q177Q7_AEDAE); contains Interpro domain(s) IPR001841 Zinc finger, RING-type " Solyc01g111980.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8987732189879732 functional_description:"Lysine/histidine transporter (AHRD V1 **** B9HR02_POPTR); contains Interpro domain(s) IPR013057 Amino acid transporter, transmembrane " ******* Solyc02g093150.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4865866148660977 functional_description:"AP2-like ethyleneresponsive transcription factor At1g16060 (AHRD V1 *-*AP2L1_ARATH); contains Interpro domain(s) IPR001471 Pathogenesis-related transcriptional factor and ERF, DNAbinding " Solyc06g065560.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3734160137343142 functional_description:"Fatty acid elongase 3ketoacyl-CoA synthase (AHRD V1 **** Q6DUV6_BRANA); contains Interpro domain(s) IPR012392 Very-long-chain 3-ketoacyl-CoA synthase " Solyc10g076250.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5847359058477404 functional_description:"Aminotransferase like protein (AHRD V1 ***- Q0WWF1_ARATH); contains Interpro domain(s) IPR005814 Aminotransferase class-III " Solyc07g041080.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:4910985949113321 functional_description:"WD repeat-containing protein 61 (AHRD V1 **-- B5XGQ3_SALSA); contains Interpro domain(s) IPR020472 G-protein beta WD-40 repeat, region " Solyc06g005500.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:526277-528874 functional_description:"ATP binding / serine-threonine kinase (AHRD V1 **** C5DB71_VITVI); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " ******* Solyc05g007050.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:16379101643686 functional_description:"ATP binding / serine-

489

7E-50

230

3E-20

710

1E-75

*******

*******

676

9E-72

455

5E-46

552

3E-57

458

2E-46

443

1E-44

*******

*******

544

2E-56


503

Les.5356.1.S1_at

407

504

Les.5367.1.S1_at

419

505

Les.5410.1.S1_at

383

506

Les.5411.1.S1_at

400

507

Les.5428.1.S1_at

432

508

Les.5431.1.S1_at

472

509

Les.5437.1.S1_at

423

510

Les.5438.1.S1_at

465

511

Les.5450.1.S1_at

494

512

Les.5454.1.S1_at

470

513

Les.5458.1.S1_at

507

threonine kinase (AHRD V1 **** C5DB71_VITVI); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " ******* Solyc07g052640.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5842699258429407 functional_description:"Glycosyltransferase-like protein (AHRD V1 **-- D8QTD2_SELML); contains Interpro domain(s) IPR006740 Protein of unknown function DUF604 " Solyc01g102350.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8294218282946739 functional_description:"Pectinacetylesterase like protein (Fragment) (AHRD V1 *--- Q56WP8_ARATH); contains Interpro domain(s) IPR004963 Pectinacetylesterase " Solyc05g024410.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:3165063731653525 functional_description:"Kelch-like protein 9 (AHRD V1 ***- KLHL9_HUMAN); contains Interpro domain(s) IPR015915 Kelch-type beta propeller " Solyc09g065200.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E0IEG gene_region:5877543258778004 functional_description:"Cyclin-dependent kinase (AHRD V1 **** A6YTD1_CUCME); contains Interpro domain(s) IPR012389 Negative regulatory factor PREG " Solyc07g007370.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:21065052112563 functional_description:"NEDD8 ultimate buster 1 (AHRD V1 **-- C0HB30_SALSA); contains Interpro domain(s) IPR009060 UBA-like " Solyc06g066800.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3837811838378855 functional_description:"Glycosyl transferase family 8 (AHRD V1 **-- B8HXH4_CYAP4)" Solyc08g042140.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:2945904029468994 functional_description:"Stress regulated protein isoform 3 (AHRD V1 **-- Q2KP22_9SOLN)" Solyc09g075160.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6244873562451605 functional_description:"60S ribosomal protein L22-2 (AHRD V1 ***- D7L3W0_ARALY); contains Interpro domain(s) IPR002671 Ribosomal protein L22e " Solyc01g100430.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8221686182219552 functional_description:"Ribosomal RNA small subunit methyltransferase A (AHRD V1 ***RSMA_CYAP8); contains Interpro domain(s) IPR011530 rRNA adenine dimethylase " Solyc08g077790.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5886807158872927 functional_description:"Peptidyl-prolyl cis-trans isomerase-like 3 (AHRD V1 *-*- PPIL3_CHICK); contains

*******

*******

208

2E-17

356

9E-35

576

3E-60

251

2E-22

607

1E-63

606

1E-63

511

1E-52

375

1E-36

505

8E-52

674

2E-71


514

Les.547.1.S1_at

118

515

Les.5470.1.S1_at

536

516

Les.5476.1.S1_at

554

517

Les.5488.1.S1_at

536

518

Les.5491.1.S1_at

412

519

Les.551.1.A1_at

106

520

Les.5510.1.S1_at

545

521

Les.5512.1.S1_at

498

522

Les.5513.1.S1_at

506

523

Les.5515.1.S1_at

512

524

Les.5523.1.S1_at

518

525

Les.5549.1.S1_at

462

Interpro domain(s) IPR002130 Peptidyl-prolyl cis-trans isomerase, cyclophilin-type " Solyc02g093590.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4897931048982160 functional_description:"CONSTANS-like zinc finger protein (AHRD V1 *-*- D0EP06_SOYBN); contains Interpro domain(s) IPR010402 CCT domain " Solyc09g064630.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H0E1IEG gene_region:5755260457553871 functional_description:"TPR domain protein (AHRD V1 *--- B6U810_MAIZE); contains Interpro domain(s) IPR011990 Tetratricopeptide-like helical " Solyc07g006520.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:13183801325425 functional_description:"Preprotein translocase secY subunit (AHRD V1 ***- A8IS14_CHLRE); contains Interpro domain(s) IPR002208 SecY protein " Solyc04g015480.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:56847305691283 functional_description:"cDNA clone 006-204-H08 full insert sequence (AHRD V1 *-*- B7E442_ORYSJ)" Solyc09g064380.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:5715710357159773 functional_description:"TPR Domain containing protein expressed (AHRD V1 **-- Q10CT3_ORYSJ)" ******* Solyc10g085040.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6368374663684345 functional_description:"Soul heme-binding family protein (AHRD V1 ***- D7LKR5_ARALY); contains Interpro domain(s) IPR006917 SOUL haembinding protein " Solyc02g070770.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3495991134963081 functional_description:"NAD-dependent epimerase/dehydratase (AHRD V1 **-- B8HW76_CYAP4); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc04g079930.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6184429361847291 functional_description:"Os10g0358600 protein (Fragment) (AHRD V1 ***- Q0IY80_ORYSJ)" Solyc04g050920.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H0E1IEG gene_region:4812818148131007 functional_description:"Os02g0504100 protein (Fragment) (AHRD V1 *-*- Q0E114_ORYSJ)" Solyc02g088390.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4506342745065755 functional_description:"Blue copper-like protein (AHRD V1 *--- B8Y8A0_GOSHI); contains Interpro domain(s) IPR003245 Plastocyanin-like " Solyc08g075810.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5707355457077764 functional_description:"Acyl-CoA

191

1E-15

556

1E-57

381

2E-37

582

1E-60

370

3E-36

*******

*******

846

3E-91

629

4E-66

496

1E-50

508

4E-52

561

3E-58

564

1E-58


526

Les.5558.1.S1_at

291

527

Les.5568.1.S1_at

447

528

Les.5579.1.S1_at

390

529

Les.56.1.S1_at

408

530

Les.5604.1.S1_at

547

531

Les.5615.1.S1_at

533

532

Les.5616.1.S1_at

374

533

Les.5628.1.S1_at

449

534

Les.5629.1.S1_at

453

535

Les.5634.1.S1_at

473

536

Les.5636.1.S1_at

455

synthetase/AMP-acid ligase II (AHRD V1 **** D0C359_9GAMM); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " ******* Solyc07g052760.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5853424758535395 functional_description:"Os09g0451700 protein (Fragment) (AHRD V1 *--- Q0J1B9_ORYSJ); contains Interpro domain(s) IPR007592 Protein of unknown function DUF573 " ******* Solyc06g075960.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4354293043543241 functional_description:"Histone H4 (AHRD V1 ***- B6T0P4_MAIZE); contains Interpro domain(s) IPR001951 Histone H4 " Solyc09g065400.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:5911328859114325 functional_description:"Kelch-like protein 14 (AHRD V1 ***- B6T7I5_MAIZE); contains Interpro domain(s) IPR015915 Kelch-type beta propeller " Solyc09g025260.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:1928115519284094 functional_description:"SAP-like protein BP-73 (AHRD V1 ***- B6SRI7_MAIZE); contains Interpro domain(s) IPR001757 ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter " Solyc06g048440.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:2752981327530901 functional_description:"GJ14616 (Fragment) (AHRD V1 ***- B4MH79_DROVI); contains Interpro domain(s) IPR010800 Glycine rich " Solyc02g064950.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3062899430634857 functional_description:"CBS domain-containing protein-like (AHRD V1 ***- B8AP73_ORYSI); contains Interpro domain(s) IPR000644 Cystathionine betasynthase, core " Solyc02g071620.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3559392835595867 functional_description:"GDSL esterase/lipase At1g29670 (AHRD V1 ***- GDL15_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc06g034040.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:2025570720256150 functional_description:"Oleosin (AHRD V1 ***A5JVA7_FICAW); contains Interpro domain(s) IPR000136 Oleosin " Solyc10g084820.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6354224363545790 functional_description:"Palmitoyltransferase PFA4 (AHRD V1 ***- B6TA04_MAIZE); contains Interpro domain(s) IPR001594 Zinc finger, DHHC-type "

*******

*******

316

5E-30

*******

*******

410

6E-41

310

4E-29

370

4E-36

402

4E-40

314

9E-30

805

1E-86

327

3E-31

179

4E-14


Les.5638.1.S1_at

479

538

Les.564.1.S1_at

406

539

Les.5648.1.S1_at

437

540

Les.5650.1.S1_at

455

541

Les.566.1.A1_at

126

542

Les.5664.1.S1_at

457

543

Les.5680.1.S1_at

514

544

Les.5692.1.S1_at

512

545

Les.5694.1.S1_at

444

546

Les.5706.1.S1_at

498

547

Les.5719.1.S1_at

476

Solyc01g109700.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8835631688359005 functional_description:"Transcription factor (AHRD V1 *-** D6MKM4_9ASPA); contains Interpro domain(s) IPR011598 Helix-loop-helix DNA-binding " Solyc05g005080.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:81637-83955 functional_description:"Endo-1 4-beta-glucanase (AHRD V1 ***- O04890_SOLLC); contains Interpro domain(s) IPR001701 Glycoside hydrolase, family 9 " Solyc11g008260.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:24871822489778 functional_description:"Cysteine proteinase cathepsin F (AHRD V1 **-- D3TN89_GLOMM); contains Interpro domain(s) IPR013128 Peptidase C1A, papain " Solyc01g057830.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:5693546156939990 functional_description:"30S ribosomal protein S1 (AHRD V1 **-- B4FUZ5_MAIZE); contains Interpro domain(s) IPR003029 Ribosomal protein S1, RNA binding domain " ******* Solyc03g083560.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4705880847059857 functional_description:"Expressed protein (Fragment) (AHRD V1 ***- B3VJP0_POPTN); contains Interpro domain(s) IPR006766 Phosphate-induced protein 1 conserved region " Solyc11g007610.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:18627261866719 functional_description:"DEAD-box ATPdependent RNA helicase 5 (AHRD V1 *-*- RH5_ORYSJ); contains Interpro domain(s) IPR011545 DNA/RNA helicase, DEAD/DEAH box type, N-terminal " Solyc09g065090.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H0E0IEG gene_region:5853441258535496 functional_description:"Unknown Protein (AHRD V1)" Solyc06g072670.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4120744841209629 functional_description:"Short-chain dehydrogenase/reductase SDR (AHRD V1 ***Q08PN0_STIAU); contains Interpro domain(s) IPR002347 Glucose/ribitol dehydrogenase " Solyc04g080550.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6227706862278733 functional_description:"Phenylcoumaran benzylic ether reductase (AHRD V1 **** B6VRE8_TOBAC); contains Interpro domain(s) IPR008030 NmrA-like " Solyc01g105310.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8528304285284590 functional_description:"Metacaspase (AHRD V1 ***- A8NU42_COPC7); contains Interpro domain(s)

702

1E-74

281

5E-26

676

1E-71

575

5E-60

*******

*******

756

5E-81

372

2E-36

379

4E-37

673

2E-71

484

2E-49

636

5E-67

Table S1 List of differentially expressed genes in rin mutant. IPR011600 Peptidase C14, caspase catalytic " 548

Les.5728.1.S1_at

402

549

Les.5748.1.S1_at

366

550

Les.5789.1.S1_at

568

551

Les.5804.1.S1_at

432

552

Les.5809.1.S1_at

521

553

Les.5817.1.S1_at

422

554

Les.5818.1.S1_at

489

555

Les.582.1.A1_at

124

556

Les.5820.1.S1_at

424

557

Les.5832.1.S1_at

435

558

Les.5842.1.S1_at

538

Solyc12g096930.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6398915963992685 functional_description:"Caleosin (AHRD V1 ***- Q9SQ57_SESIN); contains Interpro domain(s) IPR007736 Caleosin related " Solyc05g053880.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6305919563063139 functional_description:"cDNA FLJ42396 fis clone ASTRO2001107 (AHRD V1 *-*B3KW72_HUMAN)" Solyc10g008910.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:29356072936017 functional_description:"Histone H3 (AHRD V1 ***- D8L9K7_WHEAT); contains Interpro domain(s) IPR000164 Histone H3 " Solyc08g008330.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H0E1IEG gene_region:27611192765534 functional_description:"Unknown Protein (AHRD V1)" Solyc02g078580.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3782286637824803 functional_description:"Paf1/RNA polymerase II complex (AHRD V1 **-- Q2U0F7_ASPOR); contains Interpro domain(s) IPR018144 Plus-3 domain, subgroup " Solyc04g081300.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6292895362933774 functional_description:"Endoglucanase 1 (AHRD V1 ***- B6U0J0_MAIZE); contains Interpro domain(s) IPR001701 Glycoside hydrolase, family 9 " Solyc07g017240.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H0E0IEG gene_region:65683376568600 functional_description:"Unknown Protein (AHRD V1)" ******* Solyc05g055480.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6425632664259754 functional_description:"NAC-domain transcription factor (AHRD V1 *-** D3WFN5_WHEAT); contains Interpro domain(s) IPR003441 No apical meristem (NAM) protein " Solyc12g042600.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4339776443399652 functional_description:"UDP-glucosyltransferase family 1 protein (AHRD V1 ***- C6KI43_CITSI); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " Solyc09g059170.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:4917281149173542 functional_description:"Anthocyanidin 3-Oglucosyltransferase (AHRD V1 **** B6SU01_MAIZE); contains Interpro domain(s) IPR002213 UDPglucuronosyl/UDP-glucosyltransferase "

723

3E-77

585

2E-61

557

1E-57

352

3E-34

412

6E-41

374

9E-37

419

8E-42

*******

*******

493

1E-50

777

2E-83

678

9E-72


Les.5848.1.A1_at

490

560

Les.5848.2.S1_at

256

561

Les.5850.1.S1_at

467

562

Les.5853.1.S1_at

422

563

Les.5864.1.S1_at

489

564

Les.5865.1.S1_at

437

565

Les.587.1.S1_at

467

566

Les.5892.1.S1_at

370

567

Les.5917.1.S1_at

498

568

Les.5918.1.S1_at

459

569

Les.5930.1.S1_at

474

Solyc03g097030.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5282893452833486 functional_description:"4-coumarate CoA ligase (AHRD V1 **** B6F2H0_IPOBA); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc03g097030.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5282893452833486 functional_description:"4-coumarate CoA ligase (AHRD V1 **** B6F2H0_IPOBA); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc12g013710.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:45461024548577 functional_description:"Protochlorophyllide reductase (AHRD V1 ***- Q8LAV9_ARATH); contains Interpro domain(s) IPR005979 Light-dependent protochlorophyllide reductase " Solyc01g087720.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7438686474416988 functional_description:"Structural maintenance of chromosomes family protein (AHRD V1 ***D7M7H7_ARALY); contains Interpro domain(s) IPR003395 RecF/RecN/SMC protein, N-terminal " Solyc07g043420.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5450426354505514 functional_description:"2-oxoglutarate-dependent dioxygenase (AHRD V1 **-* Q9ZSH4_SOLCH); contains Interpro domain(s) IPR005123 Oxoglutarate and irondependent oxygenase " Solyc02g070800.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H0E1IEG gene_region:3498165234984067 functional_description:"Ycf23 protein (AHRD V1 ***- Q7NE74_GLOVI); contains Interpro domain(s) IPR007570 Protein of unknown function DUF561 " ******* Solyc07g065970.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:6476883364769327 functional_description:"Chaperone protein dnaJ 11 (AHRD V1 *-*- B6SS19_MAIZE); contains Interpro domain(s) IPR001623 Heat shock protein DnaJ, N-terminal " Solyc07g026650.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:3013970230140837 functional_description:"1-aminocyclopropane-1carboxylate oxidase (AHRD V1 **** Q6A1K7_SOLLC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc01g094910.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7807596978079017 functional_description:"Ferric reductase oxidase (AHRD V1 **-* D6RVS5_HORVU); contains Interpro domain(s) IPR013121 Ferric reductase, NAD binding " Solyc12g045030.1.1 genomic_reference:SL2.31ch12

398

2E-39

201

7E-17

743

2E-79

724

2E-77

782

6E-84

523

5E-54

*******

*******

458

1E-46

877

6E-95

572

1E-59

614

2E-64


570

Les.5931.1.S1_at

398

571

Les.5933.1.S1_at

300

572

Les.5934.1.S1_at

299

573

Les.5954.1.S1_at

363

574

Les.601.1.S1_at

467

575

Les.611.1.S1_at

376

576

Les.614.1.A1_at

130

577

Les.62.1.S1_at

592

578

Les.63.1.S1_at

494

579

Les.67.1.S1_at

541

580

Les.672.1.S1_at

130

581

Les.677.2.A1_at

60

evidence_code:10F1H1E1IEG gene_region:4586544445866452 functional_description:"Short-chain dehydrogenase/reductase family protein (AHRD V1 **-D7LV30_ARALY); contains Interpro domain(s) IPR002347 Glucose/ribitol dehydrogenase " ******* ******* Solyc12g044950.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4574505745746158 functional_description:"Omega-6 fatty acid desaturase (AHRD V1 **** Q461Q1_HEVBR); contains Interpro domain(s) IPR005804 Fatty acid desaturase, type 1" Solyc03g097920.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5375723153758238 functional_description:"Mitogen-activated protein kinase kinase (AHRD V1 **** D7NPU9_CAPAN); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc01g009010.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:30143873020202 functional_description:"4-diphosphocytidyl-2-Cmethyl-D- erythritol kinase (AHRD V1 ***A4USB3_NICBE); contains Interpro domain(s) IPR004424 4-diphosphocytidyl-2C-methyl-D-erythritol kinase " Solyc01g068030.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:6945816169460469 functional_description:"Cyclase/dehydrase (AHRD V1 ***- B6T2Z5_MAIZE); contains Interpro domain(s) IPR005031 Streptomyces cyclase/dehydrase " ******* Solyc08g060970.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:4335411643358621 functional_description:"Polygalacturonase (AHRD V1 **-* Q9ZPI8_SOLLC); contains Interpro domain(s) IPR012334 Pectin lyase fold " Solyc11g072310.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:5259161852594016 functional_description:"Gibberellin 20-oxidase-3 (AHRD V1 **** Q9ZPP2_SOLLC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc03g123630.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6447859464481490 functional_description:"Pectinesterase (AHRD V1 ***- Q564D7_SOLLC); contains Interpro domain(s) IPR000070 Pectinesterase, catalytic " Solyc10g080840.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6134657661348105 functional_description:"Cytochrome P450 (AHRD V1 ***- A2PZD4_IPONI); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " *******

*******

*******

*******

*******

485

8E-50

681

2E-72

731

5E-78

382

8E-38

*******

*******

1031

1E-112

756

7E-81

720

1E-76

215

2E-18

*******

*******


Les.681.1.A1_at

132

583

Les.692.1.S1_at

105

584

Les.695.1.A1_at

133

585

Les.73.1.S1_at

515

586

Les.733.1.S1_at

512

587

Les.738.1.S1_at

289

588

Les.75.1.S1_s_at

457

589

Les.790.1.A1_at

84

590

Les.796.1.A1_at

199

591

Les.797.1.S1_at

480

592

Les.827.1.S1_at

505

593

Les.857.1.S1_at

413

594

Les.876.1.A1_at

112

595

Les.886.1.A1_at

130

596

Les.899.1.S1_at

544

******* Solyc01g096740.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7951355679519654 functional_description:"Transporter major facilitator family (AHRD V1 **-- C4M254_ENTHI); contains Interpro domain(s) IPR016196 Major facilitator superfamily, general substrate transporter " ******* Solyc09g090070.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6497342464975040 functional_description:"Inorganic phosphate transporter (AHRD V1 **** O22548_SOLLC); contains Interpro domain(s) IPR004738 Phosphate permease " ******* Solyc05g007140.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:17334231736352 functional_description:"Receptor-like protein kinase At3g21340 (AHRD V1 **** RLK6_ARATH); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc06g008450.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E0IEG gene_region:23547592358589 functional_description:"Disease resistance protein RPP13 variant (AHRD V1 ***- Q1KN28_ARATH); contains Interpro domain(s) IPR002182 NB-ARC " *******

*******

*******

167

6E-13

*******

*******

293

8E-44

*******

*******

487

5E-50

691

2E-73

*******

*******

******* Solyc09g090730.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6551371965515191 functional_description:"Ammonium transporter (AHRD V1 **** Q09J80_9ROSI); contains Interpro domain(s) IPR001905 Ammonium transporter " Solyc02g089350.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4577840145779073 functional_description:"Gibberellin regulated protein (AHRD V1 **-- Q2HRH3_MEDTR); contains Interpro domain(s) IPR003854 Gibberellin regulated protein " Solyc05g049980.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:5896924158972481 functional_description:"Glycoside hydrolase family 28 protein/polygalacturonase family protein (AHRD V1 **-- Q1PF10_ARATH); contains Interpro domain(s) IPR012334 Pectin lyase fold " *******

*******

*******

442

2E-44

308

2E-33

740

3E-79

*******

*******

******* Solyc03g083440.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4688257346893660 functional_description:"Glutamate synthase (AHRD V1 **** C1E4G5_9CHLO); contains Interpro domain(s) IPR012220 Glutamate synthase, eukaryotic IPR006005 Glutamate synthase, NADH/NADPH, small

*******

*******

282

7E-26

Table S1 List of differentially expressed genes in rin mutant. subunit 1 " 597

Les.915.1.S1_at

415

598

Les.953.2.A1_at

133

599

Les.96.1.A1_at

570

600

Les.966.1.S1_at

491

601

Les.97.1.S1_at

510

602

LesAffx.1.1.S1_at

316

603

LesAffx.10172.1.S1_at

441

604

LesAffx.10176.1.A1_at

461

605


425

606


476

607


537

Solyc02g087880.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4473064544732284 functional_description:"Tubulin alpha-7 chain (AHRD V1 ***- B9IJV8_POPTR); contains Interpro domain(s) IPR002452 Alpha tubulin " ******* Solyc08g007420.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:19798191982843 functional_description:"L-lactate dehydrogenase (AHRD V1 **** Q96570_SOLLC); contains Interpro domain(s) IPR011304 L-lactate dehydrogenase " Solyc01g102400.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8298355782985524 functional_description:"Germin-like protein (AHRD V1 ***- O65358_SOLTU); contains Interpro domain(s) IPR014710 RmlC-like jelly roll fold " Solyc08g078850.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5971552759717439 functional_description:"L-lactate dehydrogenase (AHRD V1 **** Q96569_SOLLC); contains Interpro domain(s) IPR011304 L-lactate dehydrogenase " Solyc01g091170.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7662451776626246 functional_description:"Agmatinase (AHRD V1 ***- Q1IPT1_ACIBL); contains Interpro domain(s) IPR016160 Aldehyde dehydrogenase, conserved site IPR006035 Ureohydrolase " Solyc11g044470.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E0IEG gene_region:3578342235788751 functional_description:"Heterogeneous nuclear ribonucleoprotein A2/B1-like (AHRD V1 *--Q5ZDX8_ORYSJ); contains Interpro domain(s) IPR000504 RNA recognition motif, RNP-1 " Solyc03g096050.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5131784751320583 functional_description:"1-aminocyclopropane-1carboxylate oxidase 1 (AHRD V1 **-* ACCO1_SOLLC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc02g081360.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3993138939933214 functional_description:"Long-chain-fatty-acid-CoA ligase (AHRD V1 **** D0J2H7_COMT2); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc02g081360.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3993138939933214 functional_description:"Long-chain-fatty-acid-CoA ligase (AHRD V1 **** D0J2H7_COMT2); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc12g087870.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:61812725-

472

4E-48

*******

*******

392

1E-38

645

5E-68

521

1E-53

407

9E-41

581

1E-60

849

9E-92

685

8E-73

599

1E-62

464

6E-47


608


387

609


228

610


348

611


358

612


123

613

LesAffx.109.1.A1_at

534

614


438

615


114

616


386

617


423

618


482

61814392 functional_description:"Purine permease family protein (AHRD V1 **-- D7MCV2_ARALY); contains Interpro domain(s) IPR004853 Protein of unknown function DUF250 " Solyc01g109460.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8816786588170808 functional_description:"Solute carrier family 2, facilitated glucose transporter member 3 (AHRD V1 ***GTR3_RAT); contains Interpro domain(s) IPR003663 Sugar/inositol transporter " Solyc01g079670.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E0IEG gene_region:7130155771302024 functional_description:"Long cell-linked locus protein (AHRD V1 ***- B6SJT6_MAIZE)" ******* ******* Solyc06g084270.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4575620945761736 functional_description:"GTP-binding family protein (AHRD V1 ***- D7M3D0_ARALY); contains Interpro domain(s) IPR019991 GTP-binding protein, ribosome biogenesis, YlqF " Solyc02g085580.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4299001542992236 functional_description:"C2H2L domain class transcription factor (AHRD V1 **-* D9ZIU5_MALDO); contains Interpro domain(s) IPR007087 Zinc finger, C2H2-type " Solyc10g047360.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:3609531936099675 functional_description:"Polyadenylate-binding protein family protein (AHRD V1 **** D7MT99_ARALY); contains Interpro domain(s) IPR000504 RNA recognition motif, RNP-1 " Solyc10g081240.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6166658361675944 functional_description:"Protein grpE (AHRD V1 *-*- B0CAY8_ACAM1); contains Interpro domain(s) IPR000740 GrpE nucleotide exchange factor " Solyc03g097170.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5294085652943706 functional_description:"Cinnamoyl-CoA reductase-like protein (AHRD V1 ***- Q9M0B3_ARATH); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc05g010810.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:49878014989723 functional_description:"Phosphatidylinositol kinase (AHRD V1 *-** D0MQD8_PHYIN); contains Interpro domain(s) IPR000403 Phosphatidylinositol 3- and 4-kinase, catalytic " Solyc04g072400.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5701475557019388 functional_description:"Endoribonuclease E-like

628

3E-66

422

2E-42

*******

*******

*******

*******

209

8E-18

458

3E-46

705

4E-75

195

3E-16

637

2E-67

714

3E-76

375

9E-37

Table S1 List of differentially expressed genes in rin mutant. protein (AHRD V1 **-- Q656E2_ORYSJ)" 619


149

620


218

621


187

622


177

623


273

624


113

625


231

626


310

627


104

628


125

Solyc03g007600.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:21428142146082 functional_description:"Pentatricopeptide repeatcontaining protein At4g21190 (AHRD V1 ***PP332_ARATH); contains Interpro domain(s) IPR002885 Pentatricopeptide repeat " Solyc09g013150.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:55541145559440 functional_description:"Vesicular glutamate transporter 3 (AHRD V1 **-* B5AU16_DANRE); contains Interpro domain(s) IPR016196 Major facilitator superfamily, general substrate transporter " Solyc10g080680.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6121637261218459 functional_description:"Adenylyl-sulfate kinase (AHRD V1 ***- B9SHF5_RICCO); contains Interpro domain(s) IPR002891 Adenylylsulphate kinase, C-terminal " Solyc12g007030.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:14650231470759 functional_description:"Aldehyde dehydrogenase 1 (AHRD V1 ***- C5I9X1_ARTAN); contains Interpro domain(s) IPR015590 Aldehyde dehydrogenase " Solyc11g010180.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:32648823269537 functional_description:"Mitochondrial/chloroplast ribosomal protein L54/L37 (ISS) (AHRD V1 *-*Q01BU7_OSTTA); contains Interpro domain(s) IPR013870 Ribosomal protein L37, mitochondrial " ******* Solyc12g099360.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6488029364883142 functional_description:"Acyl-CoA synthetase/AMP-acid ligase II (AHRD V1 **** Q2W3Z0_MAGSA); contains Interpro domain(s) IPR000873 AMP-dependent synthetase and ligase " Solyc10g079370.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6023811760241257 functional_description:"Transcription initiation factor IIB-2 (AHRD V1 ***- D7L8X6_ARALY); contains Interpro domain(s) IPR000812 Transcription factor TFIIB related " Solyc01g005980.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:650681-652528 functional_description:"POT family domain containing protein expressed (AHRD V1 *-*- D8L9H8_WHEAT); contains Interpro domain(s) IPR007493 Protein of unknown function DUF538 " Solyc03g118060.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H0E0IEG gene_region:6109808061098794 functional_description:"Unknown Protein (AHRD V1)"

249

2E-22

359

3E-35

176

6E-14

303

1E-28

284

2E-26

*******

*******

376

4E-37

396

2E-39

175

7E-14

207

1E-17



152

630


125

631


468

632


505

633


543

634


343

635


538

636


116

637


100

638


352

Solyc03g007170.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:17442051748282 functional_description:"FK506-binding protein 4 (EC 5.2.1.8)(Peptidyl-prolyl cis-trans isomerase)(PPIase)(Rotamase) (AHRD V1 *-** C8V696_EMENI); contains Interpro domain(s) IPR001179 Peptidyl-prolyl cis-trans isomerase, FKBP-type " Solyc03g120430.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6287586862879085 functional_description:"Glycerate kinase (AHRD V1 **** C1DYY5_9CHLO)" Solyc03g118090.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6111499561118443 functional_description:"Calcium-binding mitochondrial carrier protein SCaMC-1 (AHRD V1 **** B5X2X8_SALSA); contains Interpro domain(s) IPR002113 Adenine nucleotide translocator 1 " Solyc01g007020.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:15768841578110 functional_description:"U-box domain-containing protein (AHRD V1 ***- D7LU64_ARALY); contains Interpro domain(s) IPR003613 U box domain " Solyc01g007020.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:15768841578110 functional_description:"U-box domain-containing protein (AHRD V1 ***- D7LU64_ARALY); contains Interpro domain(s) IPR003613 U box domain " Solyc08g006340.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:991350-992033 functional_description:"UDP-glucosyltransferase family 1 protein (AHRD V1 **** C6KI44_CITSI); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " Solyc08g006410.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:10117001013307 functional_description:"UDP-glucose glucosyltransferase (AHRD V1 **** B6EWX8_LYCBA); contains Interpro domain(s) IPR002213 UDPglucuronosyl/UDP-glucosyltransferase " Solyc10g080960.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6146290161463701 functional_description:"Transcription factor (Fragment) (AHRD V1 **-* D6MKQ8_9ASPA); contains Interpro domain(s) IPR006447 Myb-like DNA-binding region, SHAQKYF class " Solyc04g078910.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6117218961173256 functional_description:"Thioredoxin-like 2 (AHRD V1 *-*- B6U3H2_MAIZE); contains Interpro domain(s) IPR013766 Thioredoxin domain " Solyc12g006370.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:884199-888702 functional_description:"Amine oxidase family protein (AHRD V1 **** Q1EPI3_MUSAC); contains Interpro

207

1E-17

208

1E-17

768

2E-82

718

2E-76

742

3E-79

529

6E-55

925

1E-100

193

6E-16

166

8E-13

616

5E-65

Table S1 List of differentially expressed genes in rin mutant. domain(s) IPR002937 Amine oxidase " 639


313

640


129

641


226

642


461

643


398

644


268

645


221

646


433

647


356

648


418

Solyc12g005850.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:481937-488981 functional_description:"Multidrug resistance protein mdtK (AHRD V1 *--- MDTK_ERWAM); contains Interpro domain(s) IPR002528 Multi antimicrobial extrusion protein MatE " Solyc03g026010.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:78019947803370 functional_description:"Transmembrane protein 161B (AHRD V1 *-*- T161B_MOUSE)" Solyc01g098390.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8067847080680116 functional_description:"GID1-like gibberellin receptor (AHRD V1 **-- A7MAQ4_HORVU); contains Interpro domain(s) IPR013094 Alpha/beta hydrolase fold3" Solyc10g055200.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5195609351956677 functional_description:"Disease resistance response (AHRD V1 ***- D7KM73_ARALY); contains Interpro domain(s) IPR004265 Plant disease resistance response protein " Solyc07g051840.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5768725757690237 functional_description:"WRKY transcription factor (AHRD V1 ***- D0PSE9_9LAMI); contains Interpro domain(s) IPR003657 DNA-binding WRKY " Solyc04g076050.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5861635758619390 functional_description:"Divalent cation tolerance protein CutA (AHRD V1 *-*- Q3Z664_DEHE1); contains Interpro domain(s) IPR004323 Divalent ion tolerance protein, CutA1 " Solyc01g006450.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:10593151063123 functional_description:"Enoyl reductase (AHRD V1 ***- P93062_BRANA); contains Interpro domain(s) IPR014358 Enoyl-[acyl-carrier-protein] reductase (NADH) " Solyc01g094290.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7758119877591427 functional_description:"Glutathione-regulated potassium-efflux system protein (AHRD V1 *-*B3CM92_WOLPP); contains Interpro domain(s) IPR004771 K+/H+ exchanger " Solyc08g082180.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6220356362205445 functional_description:"Abscisic acid receptor PYL9 (AHRD V1 **-- PYL9_ARATH); contains Interpro domain(s) IPR019587 Polyketide cyclase/dehydrase " Solyc09g075890.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6302780063030068 functional_description:"Pyrimidine 5&apos-

514

3E-53

230

3E-20

402

3E-40

328

1E-62

585

3E-61

444

5E-45

350

4E-34

532

5E-55

564

6E-59

696

4E-74


649


398

650


389

651


445

652


84

653

LesAffx.187.1.S1_at

516

654


126

655


348

656


123

657


128

658


529

nucleotidase (AHRD V1 **** B4WF69_9CAUL); contains Interpro domain(s) IPR010237 Pyrimidine 5-nucleotidase " Solyc03g096290.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5170990151711007 functional_description:"Aquaporin-like protein (AHRD V1 ***- Q8W1A9_PETHY); contains Interpro domain(s) IPR012269 Aquaporin " Solyc08g006770.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:13366571338585 functional_description:"Anthocyanidin synthase (Fragment) (AHRD V1 **-* P93120_DIACA); contains Interpro domain(s) IPR005123 Oxoglutarate and irondependent oxygenase " Solyc03g119610.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H0E1IEG gene_region:6223886862239599 functional_description:"Genomic DNA chromosome 3 P1 clone MPE11 (AHRD V1 ***Q9LUA5_ARATH)" Solyc04g009860.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:31734583175118 functional_description:"1-aminocyclopropane-1carboxylate oxidase-like protein (AHRD V1 **-* Q9LTH8_ARATH); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc12g098710.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6446698864470995 functional_description:"NnrU (AHRD V1 ***Q3MCB6_ANAVT); contains Interpro domain(s) IPR009915 NnrU " Solyc12g044930.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4573248245733803 functional_description:"F-box protein PP2-B1 (AHRD V1 ***- PP2B1_ARATH); contains Interpro domain(s) IPR001810 Cyclin-like F-box " Solyc02g086970.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4411417144117672 functional_description:"Aldehyde dehydrogenase 1 (AHRD V1 **** Q84V96_LOTCO); contains Interpro domain(s) IPR015590 Aldehyde dehydrogenase " Solyc06g068940.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3915574239157001 functional_description:"C2 domain-containing protein (AHRD V1 **-- D7L7Y3_ARALY); contains Interpro domain(s) IPR018029 C2 membrane targeting protein " Solyc07g045180.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5561609955622626 functional_description:"CONSTANS-like zinc finger protein (AHRD V1 **-- D0EP07_SOYBN); contains Interpro domain(s) IPR010402 CCT domain " Solyc10g054780.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:5141439451417771 functional_description:"Acetyl esterase (AHRD V1 **-- AES_SHIFL); contains Interpro domain(s)

690

2E-73

704

4E-75

764

6E-82

148

1E-10

709

2E-75

216

1E-18

259

1E-23

216

1E-18

228

5E-20

895

6E-97

Table S1 List of differentially expressed genes in rin mutant. IPR013094 Alpha/beta hydrolase fold-3 " 659


434

660


474

661


130

662


478

663


360

664


191

665


132

666


301

667


555

668


207

Solyc12g014380.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:52616915275170 functional_description:"Glucose-6-phosphate isomerase (AHRD V1 ***- Q1PCD2_SOLLC); contains Interpro domain(s) IPR018189 Phosphoglucose isomerase, conserved site IPR001672 Phosphoglucose isomerase (PGI) " Solyc01g081570.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7327656073278776 functional_description:"Carboxyl-terminal peptidase (AHRD V1 ***- B6TV70_MAIZE); contains Interpro domain(s) IPR004314 Protein of unknown function DUF239, plant " Solyc11g008440.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:26463082649734 functional_description:"Amino acid transporter (AHRD V1 **** B9HLH9_POPTR); contains Interpro domain(s) IPR013057 Amino acid transporter, transmembrane " Solyc04g054480.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5173381651742939 functional_description:"C2 domain-containing protein-like (AHRD V1 *-*- Q67UI5_ORYSJ); contains Interpro domain(s) IPR011989 Armadillo-like helical " Solyc02g094160.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4936292149363910 functional_description:"Ribonucleosidediphosphate reductase small chain (AHRD V1 **** B6TLH5_MAIZE); contains Interpro domain(s) IPR000358 Ribonucleotide reductase " Solyc01g005990.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:653866-655330 functional_description:"Non-specific lipid-transfer protein (AHRD V1 *-*- B9REN2_RICCO); contains Interpro domain(s) IPR003612 Plant lipid transfer protein/seed storage/trypsin-alpha amylase inhibitor " Solyc09g090150.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6504021565043174 functional_description:"Legumin 11S-globulin (AHRD V1 **-- Q39770_GINBI); contains Interpro domain(s) IPR014710 RmlC-like jelly roll fold " Solyc12g042480.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4322932143230928 functional_description:"Cytochrome P450 (AHRD V1 ***- B9HFV7_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc02g077240.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3681848036821145 functional_description:"Pyruvate decarboxylase (AHRD V1 **** Q1I1D9_CITSI); contains Interpro domain(s) IPR012110 Pyruvate decarboxylase/indolepyruvate decarboxylase " Solyc06g051200.1.1 genomic_reference:SL2.31ch06

724

3E-77

735

2E-78

206

2E-17

365

1E-35

538

6E-56

216

1E-18

230

3E-20

354

1E-47

810

4E-87

345

1E-33


669


424

670


130

671


118

672


132

673


114

674


249

675


132

676


307

677


355

678


321

679


539

evidence_code:10F1H1E1IEG gene_region:3088309230885183 functional_description:"50S ribosomal protein L3 (AHRD V1 ***- D7LJX0_ARALY); contains Interpro domain(s) IPR019927 Ribosomal protein L3, bacterial/organelle-type " Solyc02g087210.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4425313644254053 functional_description:"AN1-type zinc finger protein 2B (AHRD V1 ***- B4FVR8_MAIZE); contains Interpro domain(s) IPR000058 Zinc finger, AN1-type " Solyc02g076760.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3644141236442371 functional_description:"N-(5&aposphosphoribosyl)anthranilate isomerase (AHRD V1 **** B9SQM9_RICCO); contains Interpro domain(s) IPR011060 Ribulose-phosphate binding barrel " Solyc02g067050.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3186894131870551 functional_description:"Uncharacterized ACR COG1678 family protein (AHRD V1 **-B6SSQ6_MAIZE); contains Interpro domain(s) IPR003774 Protein of unknown function DUF179 " Solyc03g043740.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:1123629511237036 functional_description:"Hydroxyproline-rich glycoprotein (AHRD V1 ***- A9YWR1_MEDTR)" ******* Solyc09g005260.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:191856-195390 functional_description:"Calcium/proton exchanger (AHRD V1 **** C4JVH2_UNCRE); contains Interpro domain(s) IPR004713 Calcium/proton exchanger " Solyc01g006090.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:754779-755627 functional_description:"rRNA processing protein Ebp2 (AHRD V1 **-- B6K460_SCHJY); contains Interpro domain(s) IPR008610 Eukaryotic rRNA processing " Solyc06g068560.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3888274538887273 functional_description:"Folate/biopterin transporter (AHRD V1 **** B5W6N2_SPIMA); contains Interpro domain(s) IPR004324 Biopterin transport-related protein BT1 " Solyc03g123390.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6431380064317765 functional_description:"Hydrolase (AHRD V1 ***- Q4PSG2_ARATH); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc03g005020.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:30244-32671 functional_description:"Lipase (AHRD V1 **** Q1XBG1_RICCO); contains Interpro domain(s) IPR006693 AB-hydrolase associated lipase region " Solyc02g088270.1.1 genomic_reference:SL2.31ch02

641

1E-67

210

6E-18

201

7E-17

162

2E-12

*******

*******

403

3E-40

230

3E-20

427

4E-43

450

9E-46

408

1E-44

731

6E-78


680


524

681


145

682


127

683


295

684


131

685


119

686


322

687


444

688

LesAffx.269.2.S1_at

151

689


241

evidence_code:10F1H1E1IEG gene_region:4499353844994584 functional_description:"Genomic DNA chromosome 5 P1 clone MUL8 (AHRD V1 ***Q9FLY2_ARATH); contains Interpro domain(s) IPR018971 Protein of unknown function DUF1997 " Solyc12g037970.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:3368656233689364 functional_description:"Peptidyl-tRNA hydrolase family protein (AHRD V1 ***- D7KGE1_ARALY); contains Interpro domain(s) IPR001328 Peptidyl-tRNA hydrolase " Solyc07g053140.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5891845858919322 functional_description:"CONSTANS-like zinc finger protein (AHRD V1 *-*- D0EP07_SOYBN); contains Interpro domain(s) IPR000315 Zinc finger, B-box " Solyc01g096150.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7901719179020321 functional_description:"NC domain-containing protein (AHRD V1 **-- A6MD14_9ORYZ); contains Interpro domain(s) IPR007053 NC " Solyc09g082860.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6394249263946106 functional_description:"Sulfate adenylyltransferase (AHRD V1 **** Q43183_SOLTU); contains Interpro domain(s) IPR002650 ATP-sulfurylase " Solyc03g078160.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4369523043696476 functional_description:"POT family domain containing protein expressed (AHRD V1 ***D8L9H8_WHEAT); contains Interpro domain(s) IPR007493 Protein of unknown function DUF538 " Solyc01g102270.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E0IEG gene_region:8285531982857350 functional_description:"Anaphase promoting complex subunit 11 (AHRD V1 ***- D7MN37_ARALY)" Solyc12g013900.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:47062584707641 functional_description:"CT099 (Fragment) (AHRD V1 **-- Q30GX2_SOLPI); contains Interpro domain(s) IPR003245 Plastocyanin-like " Solyc12g013900.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:47062584707641 functional_description:"CT099 (Fragment) (AHRD V1 **-- Q30GX2_SOLPI); contains Interpro domain(s) IPR003245 Plastocyanin-like " Solyc09g075020.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6231914562327499 functional_description:"Multidrug resistance protein ABC transporter family (AHRD V1 **-B9GS96_POPTR); contains Interpro domain(s) IPR001140 ABC transporter, transmembrane region " Solyc10g081650.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:62005772-

746

1E-79

266

2E-24

222

3E-19

509

1E-52

218

7E-19

228

5E-20

375

5E-37

221

6E-19

251

1E-22

346

1E-33


690


159

691


211

692


133

693

LesAffx.286.2.S1_a_at

332

694


487

695


360

696


129

697


122

698

LesAffx.294.1.S1_at

351

699


478

700


144

62010320 functional_description:"Carotenoid isomerase (AHRD V1 ***- D0FZ29_9ASTE); contains Interpro domain(s) IPR014101 Carotene isomerase " Solyc02g092760.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4830203248303268 functional_description:"Hydrolase alpha/beta fold family protein expressed (AHRD V1 **-* Q10J20_ORYSJ); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc09g082720.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6381682263819894 functional_description:"Aldo/keto reductase family protein (AHRD V1 **** D7KWQ9_ARALY); contains Interpro domain(s) IPR001395 Aldo/keto reductase " ******* Solyc06g074820.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4274943042751444 functional_description:"Aquaporin-like protein (AHRD V1 ***- D1M6Z5_CAPAN); contains Interpro domain(s) IPR012269 Aquaporin " Solyc09g007760.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:12956011297598 functional_description:"Aquaporin 2 (AHRD V1 ***- O65357_SAMSA); contains Interpro domain(s) IPR012269 Aquaporin " Solyc09g007760.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:12956011297598 functional_description:"Aquaporin 2 (AHRD V1 ***- O65357_SAMSA); contains Interpro domain(s) IPR012269 Aquaporin " Solyc06g008690.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:26065272607564 functional_description:"Kelch-like protein 14 (AHRD V1 ***- B6T7I5_MAIZE); contains Interpro domain(s) IPR015915 Kelch-type beta propeller " Solyc09g011240.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:45744784579389 functional_description:"Reductase 2 (AHRD V1 **** Q6TY50_HYDMC); contains Interpro domain(s) IPR020471 Aldo/keto reductase subgroup " Solyc01g099990.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8184124781842764 functional_description:"F-box protein PP2-B1 (AHRD V1 ***- PP2B1_ARATH); contains Interpro domain(s) IPR001810 Cyclin-like F-box " Solyc05g011890.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:51145165115526 functional_description:"Sulfotransferase family protein (AHRD V1 **** D7LQL2_ARALY); contains Interpro domain(s) IPR000863 Sulfotransferase " Solyc01g005470.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:322802-324851 functional_description:"Cell number regulator 10 (AHRD

274

2E-25

362

1E-35

*******

*******

584

3E-61

514

7E-53

491

6E-52

233

1E-20

212

4E-18

541

3E-56

846

2E-91

280

5E-26


701


204

702


441

703


211

704


177

705


120

706


129

707


348

708


516

709


516

710


293

V1 **-- D9HP26_MAIZE); contains Interpro domain(s) IPR006461 Protein of unknown function Cys-rich " Solyc11g012910.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:56989275704623 functional_description:"Cation transport regulator protein (AHRD V1 ***- D8J1D8_HERSS); contains Interpro domain(s) IPR006840 ChaC-like protein " Solyc11g066040.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:4879582148803307 functional_description:"U-box domaincontaining protein 13 (AHRD V1 **-- PUB13_ARATH); contains Interpro domain(s) IPR011989 Armadillo-like helical " Solyc03g118120.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6113268561133652 functional_description:"Transferase transferring glycosyl groups (AHRD V1 **-* D7MH74_ARALY)" Solyc01g098800.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8097705680981530 functional_description:"Sodium/calcium exchanger family protein (AHRD V1 *-** C5PBJ7_COCP7); contains Interpro domain(s) IPR004837 Sodium/calcium exchanger membrane region " Solyc08g082870.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6270031162702844 functional_description:"Dehydrogenase/reductase SDR family member 13 (AHRD V1 **-DHR13_HUMAN); contains Interpro domain(s) IPR002347 Glucose/ribitol dehydrogenase " Solyc10g011820.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:40669624068519 functional_description:"Delta-6 desaturase (AHRD V1 **** D2KBG7_RIBNI); contains Interpro domain(s) IPR012171 Fatty acid/sphingolipid desaturase " Solyc08g036640.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H0E1IEG gene_region:2618956026190116 functional_description:"Protein TIFY 5A (AHRD V1 ***- TIF5A_ARATH); contains Interpro domain(s) IPR010399 Tify " Solyc02g087550.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4453521344538505 functional_description:"Beta-1, 3-galactosyl-Oglycosyl-glycoprotein beta-1,6-Nacetylglucosaminyltransferase 4 (AHRD V1 *--* GCNT4_DANRE); contains Interpro domain(s) IPR003406 Glycosyl transferase, family 14 " Solyc05g010710.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E0IEG gene_region:49115824912933 functional_description:"UDP-glucosyltransferase (AHRD V1 **** D2KPG7_WHEAT); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " Solyc07g064160.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:63648501-

302

1E-28

759

2E-81

366

5E-36

240

2E-21

202

5E-17

224

1E-19

542

2E-56

207

3E-17

735

2E-78

475

1E-48


711


297

712


123

713


277

714


133

715


430

716


127

717


386

718


153

719


119

63650157 functional_description:"Thiazole biosynthetic enzyme (AHRD V1 ***- D6N3H1_GOSHI); contains Interpro domain(s) IPR002922 Thiamine biosynthesis Thi4 protein " Solyc02g093600.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4898307748983733 functional_description:"class I heat shock protein (AHRD V1 ***- Q69BI7_CARPA); contains Interpro domain(s) IPR008978 HSP20-like chaperone " Solyc03g118130.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6113502861136415 functional_description:"Rubredoxin-like protein (AHRD V1 *--- A8JGB1_CHLRE); contains Interpro domain(s) IPR004039 Rubredoxin-type Fe(Cys)4 protein " Solyc03g118860.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6170286261705961 functional_description:"UDP-Nacetylglucosamine--N- acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (AHRD V1 **** D5BLI8_ZUNPS); contains Interpro domain(s) IPR006009 Nacetylglucosaminyltransferase, MurG " Solyc01g068080.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:6951234569515155 functional_description:"Dihydroflavonol 4reductase family (AHRD V1 ***- D7MD06_ARALY); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc02g084950.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4256544342567821 functional_description:"Carboxyl methyltransferase 4 (AHRD V1 **** B0ZB58_HUMLU); contains Interpro domain(s) IPR005299 SAM dependent carboxyl methyltransferase " Solyc08g007580.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:21253722129143 functional_description:"Uncharacterized conserved membrane protein (AHRD V1 *--- A5GTT0_SYNR3); contains Interpro domain(s) IPR019634 Protein of unknown function DUF2499 " Solyc08g005610.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:477231-479421 functional_description:"Cytochrome P450 (AHRD V1 ***B9N4Y2_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc02g068320.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3287035432872352 functional_description:"2-oxoglutarate-dependent dioxygenase (AHRD V1 **-- B9GJL0_POPTR); contains Interpro domain(s) IPR005123 Oxoglutarate and irondependent oxygenase " Solyc11g011620.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:46826064688224 functional_description:"Fatty acid-binding protein-

427

4E-43

236

6E-21

459

8E-47

227

7E-20

770

1E-82

220

4E-19

565

5E-59

269

9E-25

206

2E-17


720


143

721


133

722


371

723


220

724


520

725


133

726

LesAffx.344.2.S1_at

170

727


128

728


467

like protein (AHRD V1 ***- D6FMZ4_MYCTU); contains Interpro domain(s) IPR014878 Region of unknown function DUF1794 " Solyc12g019010.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:89733888980715 functional_description:"Ubiquinone/menaquinone biosynthesis methyltransferase UbiE (AHRD V1 ***Q0ICA4_SYNS3); contains Interpro domain(s) IPR004033 UbiE/COQ5 methyltransferase " Solyc03g121040.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6332676063329309 functional_description:"Taurine catabolism dioxygenase TauD/TfdA family (AHRD V1 ***C4AZM2_BURMA); contains Interpro domain(s) IPR003819 Taurine catabolism dioxygenase TauD/TfdA " Solyc01g108030.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8716353987167762 functional_description:"Methylcrotonoyl-CoA carboxylase beta subunit (AHRD V1 **** D4XQJ0_ACIHA); contains Interpro domain(s) IPR000022 Carboxyl transferase " Solyc02g089770.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4605693846059922 functional_description:"Dihydroflavonol-4reductase (AHRD V1 ***- B6TK03_MAIZE); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc09g075950.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6307980863081538 functional_description:"Heat shock protein 1 (AHRD V1 ***- B6SXY0_MAIZE); contains Interpro domain(s) IPR013126 Heat shock protein 70 " Solyc01g111340.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8937872589381108 functional_description:"Endo-1 4-beta-xylanase (AHRD V1 **-- B6SW51_MAIZE); contains Interpro domain(s) IPR013781 Glycoside hydrolase, subgroup, catalytic core " Solyc01g111080.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8922641589227190 functional_description:"Gibberellin-regulated protein 2 (AHRD V1 *--- B6UGG6_MAIZE); contains Interpro domain(s) IPR003854 Gibberellin regulated protein " Solyc09g082240.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6344670163448518 functional_description:"Ribosomal-proteinalanine N-acetyltransferase (AHRD V1 *-** D3FS71_BACPE); contains Interpro domain(s) IPR000182 GCN5-related N-acetyltransferase " Solyc08g006780.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:13406681346142 functional_description:"Complex interacting protein 9 (AHRD V1 ***- Q8LDX3_ARATH); contains Interpro domain(s) IPR004401 Uncharacterised protein

249

2E-22

228

5E-20

639

1E-67

352

2E-34

574

2E-64

223

2E-19

229

4E-20

216

1E-18

631

2E-66

Table S1 List of differentially expressed genes in rin mutant. family UPF0133 " 729


130

730


503

731


199

732


490

733


132

734


133

735


122

736


142

737


132

738


522

Solyc01g097910.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8035410680354726 functional_description:"Rubredoxin family protein (AHRD V1 *-*- D7KP11_ARALY); contains Interpro domain(s) IPR004039 Rubredoxin-type Fe(Cys)4 protein " Solyc08g082430.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6240380662406482 functional_description:"Nucleoside diphosphate kinase (AHRD V1 ***- D5ILC3_SOLTU); contains Interpro domain(s) IPR001564 Nucleoside diphosphate kinase, core " Solyc09g008350.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:18175961821761 functional_description:"Amino acid binding protein (AHRD V1 **-- B6TMA2_MAIZE); contains Interpro domain(s) IPR002912 Amino acid-binding ACT " Solyc12g008960.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:22681442270611 functional_description:"Calmodulin-binding protein (AHRD V1 ***- A2I5F3_BETVU)" Solyc04g015100.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:52765945281503 functional_description:"Acetyl-CoA Cacetyltransferase protein (AHRD V1 **** D3YN47_9ERIC); contains Interpro domain(s) IPR002155 Thiolase " Solyc01g080410.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7216565772166258 functional_description:"Peptide methionine sulfoxide reductase msrB (AHRD V1 ***B6T2C6_MAIZE); contains Interpro domain(s) IPR002579 Methionine sulphoxide reductase B " Solyc03g044200.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:1242132512424251 functional_description:"Alcohol dehydrogenase (AHRD V1 **** Q43169_SOLTU); contains Interpro domain(s) IPR002085 Alcohol dehydrogenase superfamily, zinc-containing " Solyc11g028020.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:1651735616525480 functional_description:"Agamous MADS-box transcription factor (AHRD V1 ***- B2CDE2_9ASPA); contains Interpro domain(s) IPR002100 Transcription factor, MADS-box IPR002487 Transcription factor, K-box " Solyc03g093430.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4816108348165673 functional_description:"Rho GTPase activating protein 1 (AHRD V1 *-** Q568D8_DANRE); contains Interpro domain(s) IPR000198 RhoGAP " Solyc12g017460.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6721547-

213

3E-18

689

4E-73

336

2E-32

891

1E-96

209

8E-18

239

3E-21

218

7E-19

229

4E-20

201

7E-17

566

2E-73


739


129

740


210

741


367

742


197

743


181

744


525

745


140

746


285

747


105

6722656 functional_description:"GDSL esterase/lipase At1g28590 (AHRD V1 ***- GDL8_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc05g047530.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:5815908658160762 functional_description:"Cytochrome P450 cinnamate 4-hydroxylase (AHRD V1 **-* A9PBZ7_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc01g090360.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H0E1IEG gene_region:7582161775822145 functional_description:"Non-specific lipidtransfer protein (AHRD V1 ***- B9RD07_RICCO); contains Interpro domain(s) IPR013770 Plant lipid transfer protein and hydrophobic protein, helical " Solyc06g065210.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3705054437054328 functional_description:"Neutral invertase like protein (AHRD V1 ***- Q67XD9_ARATH); contains Interpro domain(s) IPR006937 Plant neutral invertase " Solyc04g005630.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:411358-414033 functional_description:"Mitochondrial transcription termination factor family protein (AHRD V1 **-D7M3B1_ARALY); contains Interpro domain(s) IPR003690 Mitochodrial transcription termination factorrelated " Solyc09g015830.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:1127585111277800 functional_description:"Receptor protein kinaselike protein (AHRD V1 **** Q8VZH5_CAPAN); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc03g033840.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:97252539727808 functional_description:"26S protease regulatory subunit 6B homolog (AHRD V1 *--- PRS6B_ASPNG); contains Interpro domain(s) IPR003959 ATPase, AAAtype, core " Solyc02g092290.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H0E1IEG gene_region:4799283947996919 functional_description:"F-box/LRR-repeat protein At5g02910 (AHRD V1 ***- FBL79_ARATH); contains Interpro domain(s) IPR001810 Cyclin-like F-box " Solyc08g081570.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:6175124661755699 functional_description:"2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase (AHRD V1 **** A9ZN13_HEVBR); contains Interpro domain(s) IPR003526 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, core " Solyc02g055440.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:26960018-

232

2E-20

251

1E-22

647

1E-68

341

4E-33

331

6E-32

891

2E-96

241

2E-21

370

2E-36

167

6E-13


748


130

749


112

750


129

751


141

752


205

753


128

754


521

755


288

756


324

757


464

26961086 functional_description:"Genomic DNA chromosome 3 P1 clone MPN9 (AHRD V1 ***Q9LT28_ARATH)" Solyc03g033980.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E0IEG gene_region:99580499960035 functional_description:"Tubby-like F-box protein 5 (AHRD V1 ***- TLP5_ORYSJ); contains Interpro domain(s) IPR000007 Tubby, C-terminal " Solyc11g008440.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:26463082649734 functional_description:"Amino acid transporter (AHRD V1 **** B9HLH9_POPTR); contains Interpro domain(s) IPR013057 Amino acid transporter, transmembrane " Solyc06g073290.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4154810541548896 functional_description:"Gun4-like protein (AHRD V1 *-*- D8RVB0_SELML); contains Interpro domain(s) IPR008629 GUN4-like " Solyc06g073620.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4181276641814209 functional_description:"Molybdopterin synthase catalytic subunit (AHRD V1 **** MOC2B_ARATH); contains Interpro domain(s) IPR003448 Molybdopterin biosynthesis MoaE " Solyc12g008490.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:18933111902784 functional_description:"Ceramide glucosyltransferase (AHRD V1 ***- Q946Y1_GOSAR)" Solyc05g008820.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:30524423055249 functional_description:"Lipid phosphate phosphatase 3 (AHRD V1 **** B6SSC1_MAIZE); contains Interpro domain(s) IPR000326 Phosphatidic acid phosphatase type 2/haloperoxidase " Solyc03g117590.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6075579060756719 functional_description:"Chaperone protein dnaJ (AHRD V1 *-*- C5UZI2_CLOBO); contains Interpro domain(s) IPR001623 Heat shock protein DnaJ, N-terminal " Solyc01g086640.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7337936773382681 functional_description:"Os03g0169000 protein (Fragment) (AHRD V1 ***- Q0DUS7_ORYSJ); contains Interpro domain(s) IPR004348 Protein of unknown function DUF246, plant " Solyc04g080540.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H0E1IEG gene_region:6226855562269703 functional_description:"ST225 (AHRD V1 ***B4YYB7_THEHA)" Solyc03g118540.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6148370361486814 functional_description:"Protein TIFY 6B (AHRD

204

3E-17

169

4E-13

200

9E-17

214

2E-18

368

3E-36

223

2E-19

663

4E-70

497

3E-51

483

1E-49

754

1E-80


758


453

759


299

760


340

761


133

762


131

763


118

764


247

765


144

766


186

767


130

768


475

769


212

V1 **-- TIF6B_ARATH); contains Interpro domain(s) IPR010399 Tify " Solyc09g008830.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:22510262258540 functional_description:"Os01g0318400 protein (Fragment) (AHRD V1 *-*- Q7XXQ7_ORYSJ)" ******* Solyc05g051020.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6036331160364148 functional_description:"Dihydroflavonol 4reductase family (AHRD V1 ***- D7LCI9_ARALY); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc11g013810.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:71739337178050 functional_description:"Nitrate reductase (AHRD V1 ***- Q8LT13_SOLTU); contains Interpro domain(s) IPR012137 Nitrate reductase NADH dependant " Solyc10g008600.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:26901552692914 functional_description:"Unknown Protein (AHRD V1)" Solyc03g119980.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6254539162547481 functional_description:"Lipase-like protein (AHRD V1 **-- Q9M3D1_ARATH)" Solyc04g071800.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5639715456398772 functional_description:"Cytochrome P450 (AHRD V1 ***- B9N7D9_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc04g071780.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:5636820756370492 functional_description:"Cytochrome P450 (AHRD V1 ***- B9N7D9_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc03g097470.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5324880553261374 functional_description:"3-oxoacyl- (AHRD V1 ***- D5A3B9_SPIPL); contains Interpro domain(s) IPR004655 Beta-ketoacyl-acyl carrier protein synthase III (FabH) " Solyc09g057760.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E0IEG gene_region:4609190546094014 functional_description:"Plant-specific domain TIGR01615 family protein (AHRD V1 *-*B4FP41_MAIZE); contains Interpro domain(s) IPR006502 Protein of unknown function DUF506, plant " Solyc08g079090.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5990142659904926 functional_description:"Laccase-22 (AHRD V1 **-- LAC22_ORYSJ); contains Interpro domain(s) IPR001117 Multicopper oxidase, type 1 " Solyc08g068290.1.1 genomic_reference:SL2.31ch08

591

7E-62

*******

*******

312

9E-30

218

7E-19

244

7E-22

203

4E-17

404

2E-40

203

4E-17

299

3E-28

180

2E-14

458

2E-46

339

7E-33


770


133

771


408

772


124

773


472

774


127

775


72

776


128

777


469

778


86

779


122

evidence_code:10F1H1E1IEG gene_region:5459724154602270 functional_description:"Os01g0786800 protein (Fragment) (AHRD V1 ***- Q0JIP0_ORYSJ); contains Interpro domain(s) IPR002781 Protein of unknown function DUF81 " Solyc04g077850.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6032132560323259 functional_description:"U-box domaincontaining protein 4 (AHRD V1 **-- PUB4_ARATH); contains Interpro domain(s) IPR011989 Armadillo-like helical " Solyc01g086920.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7358848973588983 functional_description:"LRR receptor-like serine/threonine-protein kinase FEI 1 (AHRD V1 **-* FEI1_ARATH); contains Interpro domain(s) IPR001611 Leucine-rich repeat " Solyc02g061790.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H0E1IEG gene_region:2788396727886989 functional_description:"Activated RNA polymerase II transcriptional coactivator p15 (AHRD V1 **** C1BJV8_OSMMO); contains Interpro domain(s) IPR003173 Transcriptional coactivator p15 " Solyc04g082270.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6358672463588005 functional_description:"CM0216.210.nc protein (AHRD V1 ***- B0BLH4_LOTJA); contains Interpro domain(s) IPR004320 Protein of unknown function DUF241, plant " Solyc03g120550.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6297477662979122 functional_description:"Peptide transporter 1 (AHRD V1 **-* Q7XAC3_VICFA); contains Interpro domain(s) IPR000109 TGF-beta receptor, type I/II extracellular region " ******* Solyc04g007260.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:976338-981897 functional_description:"Thioesterase superfamily (AHRD V1 *-** Q0YNY9_9CHLB); contains Interpro domain(s) IPR006683 Thioesterase superfamily " Solyc00g007060.1.1 genomic_reference:SL2.31ch00 evidence_code:10F0H1E1IEG gene_region:66749246679895 functional_description:"Serine/threonine kinaselike protein ABC1063 (AHRD V1 **** Q1KMP8_HORVD); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " ******* Solyc07g005580.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:458171-463899 functional_description:"1-acyl-sn-glycerol-3-phosphate acyltransferase (AHRD V1 **** A0LIN1_SYNFM); contains Interpro domain(s) IPR004552 1-acyl-sn-glycerol3-phosphate acyltransferase "

170

3E-13

577

2E-60

207

1E-17

722

5E-77

212

4E-18

*******

*******

198

2E-16

793

3E-85

*******

*******

210

6E-18



124

781


131

782


101

783


421

784


111

785


156

786


119

787


126

788


475

789


131

790


548

791


412

Solyc03g097550.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5332476053332673 functional_description:"Pseudouridine synthase family protein (AHRD V1 ***- D7MQX8_ARALY); contains Interpro domain(s) IPR006225 Pseudouridine synthase, RluC/RluD " Solyc03g019820.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:67379166738916 functional_description:"Aquaporin (AHRD V1 ***- D6BRE1_9ROSI); contains Interpro domain(s) IPR012269 Aquaporin " Solyc01g106090.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8584134885844066 functional_description:"Photosystem II oxygen evolving complex protein PsbP (AHRD V1 *-*B8HJK6_CYAP4); contains Interpro domain(s) IPR002683 Photosystem II oxygen evolving complex protein PsbP " Solyc12g013690.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:45336284536361 functional_description:"Monooxygenase FADbinding protein (AHRD V1 **-- Q1B616_MYCSS); contains Interpro domain(s) IPR003042 Aromatic-ring hydroxylase-like " ******* Solyc04g081250.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6285301262853461 functional_description:"Auxin-induced SAURlike protein (AHRD V1 *-*- Q8S349_CAPAN); contains Interpro domain(s) IPR003676 Auxin responsive SAUR protein " ******* Solyc03g005330.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:194233-195519 functional_description:"CBL-interacting protein kinase 20 (AHRD V1 **** C4P7W9_VITVI); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc06g076300.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:4379626343797436 functional_description:"Pyrimidine 5&aposnucleotidase (AHRD V1 **** B0T131_CAUSK); contains Interpro domain(s) IPR010237 Pyrimidine 5-nucleotidase " Solyc08g079480.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6016392060164659 functional_description:"Unknown Protein (AHRD V1); contains Interpro domain(s) IPR009902 Protein of unknown function DUF1442 " Solyc10g076510.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:5882902658831573 functional_description:"Pyruvate decarboxylase (AHRD V1 **** B0ZS79_PRUAR); contains Interpro domain(s) IPR012110 Pyruvate decarboxylase/indolepyruvate decarboxylase " Solyc06g076750.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:44050817-

228

5E-20

205

2E-17

161

3E-12

687

5E-73

*******

*******

221

3E-19

*******

*******

226

9E-20

610

5E-64

233

1E-20

907

2E-98

700

1E-74


792


365

793


269

794


215

795


266

796


169

797


300

798


454

799


186

800


248

801


493

44054202 functional_description:"Peptide transporter (AHRD V1 **-* O48542_HORVU); contains Interpro domain(s) IPR000109 TGF-beta receptor, type I/II extracellular region " Solyc01g073680.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H0E1IEG gene_region:7029567770296920 functional_description:"Non-specific lipidtransfer protein (AHRD V1 ***- C6TMC6_SOYBN); contains Interpro domain(s) IPR013770 Plant lipid transfer protein and hydrophobic protein, helical " Solyc02g082900.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4110995741112535 functional_description:"Strictosidine synthase family protein (AHRD V1 **-- D7LTU8_ARALY); contains Interpro domain(s) IPR004141 Strictosidine synthase " Solyc02g067530.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3227344432277749 functional_description:"Prolyl 4-hydroxylase alpha subunit-like protein (AHRD V1 ***Q9LSI6_ARATH); contains Interpro domain(s) IPR006620 Prolyl 4-hydroxylase, alpha subunit " Solyc11g007130.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H0E1IEG gene_region:15833581588068 functional_description:"Major facilitator superfamily MFS_1 (AHRD V1 **-- C6ASI0_RHILS); contains Interpro domain(s) IPR016196 Major facilitator superfamily, general substrate transporter " Solyc10g052510.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:4831597848317728 functional_description:"Isoflavone reductase-like protein 5 (AHRD V1 ***- Q3KN68_VITVI); contains Interpro domain(s) IPR008030 NmrA-like " Solyc04g007660.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:13543211355430 functional_description:"SMP30/Gluconolaconase/LRE domain protein (AHRD V1 ***A5FD91_FLAJ1); contains Interpro domain(s) IPR013658 SMP-30/Gluconolaconase/LRE-like region " Solyc01g073820.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7042140670422185 functional_description:"CHP-rich zinc finger protein-like (AHRD V1 **-- Q9FNE5_ARATH); contains Interpro domain(s) IPR011424 C1-like " Solyc01g090810.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7628248176284099 functional_description:"Expansin protein (AHRD V1 ***- Q14F61_WHEAT); contains Interpro domain(s) IPR007112 Expansin 45, endoglucanase-like " Solyc07g056200.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H0E1IEG gene_region:6137503761375654 functional_description:"NBS-LRR class disease resistance protein (AHRD V1 **-- D5L9G6_ORYSI)" Solyc08g074940.1.1 genomic_reference:SL2.31ch08

566

3E-59

410

4E-41

363

1E-35

444

5E-45

276

1E-25

523

3E-54

868

6E-94

323

5E-31

400

6E-40

836

4E-91


802


149

803


332

804


328

805


119

806


131

807


288

808


133

809


132

810


161

811


129

evidence_code:10F0H1E1IEG gene_region:5623652656238009 functional_description:"Aspartic proteinase nepenthesin-2 (AHRD V1 **-- B6SMJ5_MAIZE); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc04g009960.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:32800693283807 functional_description:"L-allo-threonine aldolase (AHRD V1 **** D7RJ69_CARPA); contains Interpro domain(s) IPR001597 Aromatic amino acid betaeliminating lyase/threonine aldolase " Solyc02g085170.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4273137042736931 functional_description:"Glucose transporter 8 (AHRD V1 ***- Q2KKJ3_SOLIN); contains Interpro domain(s) IPR003663 Sugar/inositol transporter " Solyc01g108530.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8758999787591283 functional_description:"Acetyl esterase (AHRD V1 *--- AES_SALPB); contains Interpro domain(s) IPR013094 Alpha/beta hydrolase fold-3 " Solyc01g111380.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8941074889411439 functional_description:"Actin depolymerizing factor 5 (AHRD V1 **** A1XJ48_GOSHI); contains Interpro domain(s) IPR002108 Actin-binding, cofilin/tropomyosin type " Solyc06g062430.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3576611135769121 functional_description:"Inositol oxygenase (AHRD V1 **** A5FF81_FLAJ1); contains Interpro domain(s) IPR007828 Protein of unknown function DUF706 " Solyc03g111550.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5620283556205005 functional_description:"GDSL esterase/lipase At3g48460 (AHRD V1 ***- GDL57_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc04g064720.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5497960854982875 functional_description:"Maltose excess protein 1like, chloroplastic (AHRD V1 **** MEX1_ORYSJ)" Solyc03g118650.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:6157545661577315 functional_description:"Aldose 1-epimerase-like protein (AHRD V1 **** Q9LVH6_ARATH); contains Interpro domain(s) IPR015443 Aldose-1-epimerase " Solyc02g089540.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4590250045904767 functional_description:"CONSTANS (Fragment) (AHRD V1 **-- A6YCH7_SOLTU); contains Interpro domain(s) IPR010402 CCT domain " Solyc10g050880.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:4660382646604764 functional_description:"Gibberellin receptor

236

6E-21

304

8E-29

574

4E-60

193

6E-16

244

7E-22

511

8E-53

246

4E-22

227

7E-20

304

8E-29

225

1E-19


812


431

813


133

814


276

815


556

816


237

817


512

818


99

819


115

820


130

821


220

GID1L2 (AHRD V1 **-- B6TIA5_MAIZE); contains Interpro domain(s) IPR013094 Alpha/beta hydrolase fold3" Solyc10g081730.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:6207315862075481 functional_description:"Os02g0200800 protein (Fragment) (AHRD V1 *-*- Q0E303_ORYSJ); contains Interpro domain(s) IPR009675 Targeting for Xklp2 " Solyc07g005520.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:408207-409532 functional_description:"Potassium channel tetramerization domain-containing protein (AHRD V1 ***D7LHH7_ARALY); contains Interpro domain(s) IPR003131 Potassium channel, voltage dependent, Kv, tetramerisation " Solyc08g077530.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5868383158686794 functional_description:"Beta-amylase (AHRD V1 **** Q5F305_SOYBN); contains Interpro domain(s) IPR001371 Glycoside hydrolase, family 14B, plant " Solyc02g067840.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3252704732530658 functional_description:"Sucrase/ferredoxin domain protein (AHRD V1 *--- A1CK27_ASPCL); contains Interpro domain(s) IPR009737 Sucraseferredoxinlike " Solyc05g011970.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:51799955182212 functional_description:"Cytochrome P450 (AHRD V1 ***- B9HWV8_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc07g052430.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5826362458266148 functional_description:"Transmembrane protein 97 (AHRD V1 *-*- TMM97_HUMAN); contains Interpro domain(s) IPR016964 Transmembrane protein 97, predicted " Solyc11g011590.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:46490924650410 functional_description:"FIP1 (AHRD V1 **-B6U778_MAIZE); contains Interpro domain(s) IPR004182 GRAM " Solyc10g009000.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:30324763039032 functional_description:"snRNA-activating protein complex subunit 3 (AHRD V1 *-*- B0WT21_CULQU)" Solyc06g009170.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:31086163113031 functional_description:"Epoxide hydrolase 1 (AHRD V1 **** D8L7V7_PRUPE); contains Interpro domain(s) IPR000639 Epoxide hydrolase-like " Solyc08g082060.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6213160962135483 functional_description:"Leaf senescence protein-

620

3E-65

241

2E-21

464

2E-47

998

1E-109

407

9E-41

284

4E-26

163

2E-12

200

9E-17

225

1E-19

405

1E-40


822


440

823


266

824


402

825


200

826


204

827


317

828


133

829


131

830


133

831


102

like (AHRD V1 ***- Q654T8_ORYSJ); contains Interpro domain(s) IPR004253 Protein of unknown function DUF231, plant " Solyc11g013310.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:62718056276629 functional_description:"Auxin transporter-like protein 3 (AHRD V1 ***- B6TPT6_MAIZE); contains Interpro domain(s) IPR013057 Amino acid transporter, transmembrane " Solyc03g082890.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4633149646334048 functional_description:"Pentapeptide repeat protein (AHRD V1 *-*- B4WQI2_9SYNE); contains Interpro domain(s) IPR001646 Pentapeptide repeat " Solyc12g008640.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:20183692021783 functional_description:"Gammaglutamyltransferase-like protein (AHRD V1 ***Q9M0G0_ARATH); contains Interpro domain(s) IPR000101 Gamma-glutamyltranspeptidase " Solyc07g042320.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5279684052808095 functional_description:"3-oxoacyl-(Acyl carrier protein) synthase II (AHRD V1 **** D6YNQ6_CHLT1); contains Interpro domain(s) IPR017568 3-oxoacyl-[acylcarrier-protein] synthase 2 " Solyc12g006230.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:746869-747120 functional_description:"RING-H2 finger protein (AHRD V1 ***- Q30D22_PONTR); contains Interpro domain(s) IPR018957 Zinc finger, C3HC4 RING-type " Solyc02g086270.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4355827043564267 functional_description:"Receptor-like kinase (AHRD V1 *-*- A7VM25_MARPO); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc03g098100.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5388871353889650 functional_description:"Reductase 2 (AHRD V1 ***- Q6TY50_HYDMC); contains Interpro domain(s) IPR020471 Aldo/keto reductase subgroup " Solyc09g063070.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H0E1IEG gene_region:5665851356663410 functional_description:"Senescence-associated protein-like (ISS) (AHRD V1 ***- Q00X72_OSTTA)" Solyc12g013820.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:46045954610901 functional_description:"Ubiquitin-conjugating enzyme 23 (AHRD V1 *-*- D7L425_ARALY); contains Interpro domain(s) IPR000608 Ubiquitin-conjugating enzyme, E2 " Solyc07g053720.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5946666059470049 functional_description:"Tyrosine

758

3E-81

454

3E-46

694

6E-74

346

1E-33

389

1E-38

530

5E-55

208

1E-17

222

3E-19

241

2E-21

163

2E-12


832


348

833


205

834


90

835


307

836


133

837


448

838


116

839


354

840


547

841


512

aminotransferase-like protein (AHRD V1 **** Q9LVY1_ARATH); contains Interpro domain(s) IPR005958 Tyrosine/nicotianamine aminotransferase " Solyc11g018800.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:95969599598242 functional_description:"Peroxidase 2 (AHRD V1 ***- Q9SSZ8_SCUBA); contains Interpro domain(s) IPR002016 Haem peroxidase, plant/fungal/bacterial " Solyc02g065280.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3102042131025780 functional_description:"Methyl jasmonate esterase (AHRD V1 **-* Q56SE1_SOLTU); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc03g070380.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:3916145039166069 functional_description:"Methyl jasmonate esterase (AHRD V1 **-* Q56SE1_SOLTU); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc01g010020.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:46574684657953 functional_description:"Calmodulin (AHRD V1 ***- B6SJJ2_MAIZE); contains Interpro domain(s) IPR003299 Flagellar calcium-binding protein (calflagin) " Solyc04g082920.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6399491363999554 functional_description:"Chlorophyll a-b binding protein, chloroplastic (AHRD V1 **** CB2_PHYPA); contains Interpro domain(s) IPR001344 Chlorophyll A-B binding protein " Solyc02g086890.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4406848444069891 functional_description:"Calcium homeostasis regulator chor1 (Fragment) (AHRD V1 *-*A6N1L7_ORYSI)" Solyc03g119810.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H0E1IEG gene_region:6244127362441728 functional_description:"Unknown Protein (AHRD V1)" Solyc06g065330.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3712810937132777 functional_description:"Ring finger protein 13 (AHRD V1 ***- Q66JJ1_XENTR); contains Interpro domain(s) IPR003137 Protease-associated PA " Solyc07g042390.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5285287352853436 functional_description:"Pectinesterase (AHRD V1 **** B7SIX2_9CONI); contains Interpro domain(s) IPR006501 Pectinesterase inhibitor " Solyc07g063880.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6346030563463803 functional_description:"Beta-glucosidase (AHRD V1 ***- D3YJ59_VITVI); contains Interpro domain(s)

529

6E-55

247

3E-22

166

8E-13

292

2E-27

236

6E-21

572

1E-59

210

6E-18

458

1E-46

751

3E-80

900

1E-97

Table S1 List of differentially expressed genes in rin mutant. IPR001360 Glycoside hydrolase, family 1 " 842


431

843


563

844


514

845


127

846


116

847


100

848


334

849


335

850


336

851


398

Solyc06g050630.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:2985686829858277 functional_description:"Prephenate dehydrogenase family protein (AHRD V1 ***D7KDI5_ARALY); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc07g042590.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5337946253384158 functional_description:"ATP binding / serinethreonine kinase (AHRD V1 **** C5DB71_VITVI); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc03g005580.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:421482-424275 functional_description:"Legumin 11S-globulin (AHRD V1 **-- Q39770_GINBI); contains Interpro domain(s) IPR014710 RmlC-like jelly roll fold " Solyc11g069570.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5127230951275967 functional_description:"Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG (AHRD V1 **-- LOG_ORYSJ); contains Interpro domain(s) IPR005269 Conserved hypothetical protein CHP00730 " Solyc08g007820.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:23268012327535 functional_description:"Ethylene-responsive transcription factor 10 (AHRD V1 *-** ERF77_ARATH); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc02g065240.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3099350430995001 functional_description:"Hydrolase alpha/beta fold family protein (AHRD V1 **-- D7LG04_ARALY); contains Interpro domain(s) IPR000073 Alpha/beta hydrolase fold-1 " Solyc01g100760.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8247517982475673 functional_description:"Susceptibility homeodomain transcription factor (Fragment) (AHRD V1 *-*- Q8SAA7_ORYSA); contains Interpro domain(s) IPR007493 Protein of unknown function DUF538 " Solyc09g005120.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:70599-75524 functional_description:"Chaperone protein DnaJ (AHRD V1 *-*- C7DHA9_9EURY); contains Interpro domain(s) IPR003095 Heat shock protein DnaJ " Solyc01g108560.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E0IEG gene_region:8759479887595703 functional_description:"Acetyl esterase (AHRD V1 *--- AES_SHIFL); contains Interpro domain(s) IPR013094 Alpha/beta hydrolase fold-3 " Solyc12g042480.1.1 genomic_reference:SL2.31ch12

748

4E-80

534

5E-55

779

2E-83

216

1E-18

148

1E-10

165

1E-12

503

7E-52

373

8E-37

570

1E-59

707

2E-75


852


133

853


430

854


158

855


162

856


133

857


128

858


121

859


215

860


223

evidence_code:10F0H1E1IEG gene_region:4322932143230928 functional_description:"Cytochrome P450 (AHRD V1 ***- B9HFV7_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc01g091200.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7664939076650697 functional_description:"NAD dependent epimerase/dehydratase family protein expressed (AHRD V1 ***- Q2MJA7_ORYSJ); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc12g049580.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4666451946668741 functional_description:"Methylthioribose-1phosphate isomerase (AHRD V1 ***- MTNA_CLOTH); contains Interpro domain(s) IPR000649 Initiation factor 2B related " Solyc10g086420.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6456538464566886 functional_description:"SLT1 protein (AHRD V1 **-- Q9FQY3_TOBAC); contains Interpro domain(s) IPR008978 HSP20-like chaperone " Solyc10g086420.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6456538464566886 functional_description:"SLT1 protein (AHRD V1 **-- Q9FQY3_TOBAC); contains Interpro domain(s) IPR008978 HSP20-like chaperone " Solyc01g090890.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7635605376358268 functional_description:"Xenotropic and polytropic retrovirus receptor (AHRD V1 **-B2GU54_XENTR); contains Interpro domain(s) IPR004331 SPX, N-terminal " Solyc11g007200.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:16219861623966 functional_description:"Copper chaperone (AHRD V1 *-*- D3GC04_9ROSI); contains Interpro domain(s) IPR006121 Heavy metal transport/detoxification protein " Solyc05g010010.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:42150124215788 functional_description:"Plant-specific domain TIGR01570 family protein (AHRD V1 ***B6U2A5_MAIZE); contains Interpro domain(s) IPR006460 Protein of unknown function DUF617, plant " Solyc05g009370.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:35186403524220 functional_description:"50S ribosomal protein L15 (AHRD V1 *-*- B4B3P1_9CHRO); contains Interpro domain(s) IPR005749 Ribosomal protein L15, bacterialtype " Solyc06g061170.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3556832235569744 functional_description:"Solute carrier family 25 (Mitochondrial carrier ornithine transporter) member 15 (AHRD V1 **** Q2KHW4_BOVIN); contains Interpro

173

1E-13

593

4E-62

246

4E-22

255

4E-23

222

3E-19

183

8E-15

205

2E-17

356

7E-35

368

3E-36

Table S1 List of differentially expressed genes in rin mutant. domain(s) IPR002067 Mitochondrial carrier protein " 861


322

862


210

863


449

864


321

865


317

866


310

867


298

868


237

869


355

870


333

Solyc01g087540.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7424292474244931 functional_description:"Os01g0611000 protein (Fragment) (AHRD V1 ***- Q0JLB5_ORYSJ); contains Interpro domain(s) IPR006946 Protein of unknown function DUF642 " Solyc05g013660.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:69593716963490 functional_description:"Lysine ketoglutarate reductase trans-splicing related 1 (AHRD V1 ***B6TJT7_MAIZE); contains Interpro domain(s) IPR007877 Protein of unknown function DUF707 " Solyc08g077060.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5816159458164919 functional_description:"Zinc finger protein LSD1 (AHRD V1 **-- Q6QUK7_ORYSJ); contains Interpro domain(s) IPR005735 Zinc finger, LSD1-type " Solyc01g100930.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8258868482591569 functional_description:"GDSL esterase/lipase At1g09390 (AHRD V1 ***- GDL2_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc02g070020.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3438683134388270 functional_description:"UDP-glucosyltransferase (AHRD V1 **-* Q8LKG3_STERE); contains Interpro domain(s) IPR002213 UDP-glucuronosyl/UDPglucosyltransferase " Solyc04g082720.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6389297363894045 functional_description:"Small heat shock protein (AHRD V1 ***- A2A1W7_TOBAC); contains Interpro domain(s) IPR008978 HSP20-like chaperone " Solyc06g060570.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3496323234965871 functional_description:"Ovarian cancerassociated gene 2 protein homolog (AHRD V1 **-B5X7T4_SALSA); contains Interpro domain(s) IPR005645 Protein of unknown function DUF341 " Solyc12g010730.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:36466893649048 functional_description:"Os08g0100600 protein (Fragment) (AHRD V1 *-*- Q0J8P7_ORYSJ); contains Interpro domain(s) IPR008507 Protein of unknown function DUF789 " Solyc05g054410.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6348488963488579 functional_description:"Telomere binding protein (AHRD V1 **** A0JBS3_SOLLC); contains Interpro domain(s) IPR001005 SANT, DNA-binding " Solyc12g005350.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:216225-218423 functional_description:"Dihydroflavonol-4-reductase

541

3E-56

405

2E-40

558

5E-58

581

6E-61

539

4E-56

479

4E-49

463

3E-47

398

1E-39

581

6E-61

497

3E-51


871


132

872


114

873


344

874


125

875


190

876


154

877


130

878


502

879


130

880


296

(AHRD V1 ***- B6TUD3_MAIZE); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc09g065240.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:5889653258897981 functional_description:"Patatin-like protein 3 (AHRD V1 ***- B6TPQ5_MAIZE); contains Interpro domain(s) IPR002641 Patatin " Solyc09g010660.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:39842293988934 functional_description:"Beta-1-3-galactosyl-oglycosyl- glycoprotein (AHRD V1 **-* B6Z261_WHEAT); contains Interpro domain(s) IPR003406 Glycosyl transferase, family 14 " Solyc11g010450.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:34993993505589 functional_description:"Phosphofructokinase family protein (AHRD V1 ***- D7LE10_ARALY); contains Interpro domain(s) IPR012004 Pyrophosphatedependent phosphofructokinase TP0108 " Solyc04g009960.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:32800693283807 functional_description:"L-allo-threonine aldolase (AHRD V1 **** D7RJ69_CARPA); contains Interpro domain(s) IPR001597 Aromatic amino acid betaeliminating lyase/threonine aldolase " Solyc09g042770.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:3012127130123561 functional_description:"Rhodanese-like (AHRD V1 **-- A2Q5X2_MEDTR); contains Interpro domain(s) IPR001763 Rhodanese-like " Solyc05g009320.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:34546303455832 functional_description:"LOB domain protein 42 (AHRD V1 ***- D7KWD0_ARALY); contains Interpro domain(s) IPR004883 Lateral organ boundaries, LOB " Solyc01g109930.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8852296188527414 functional_description:"Inositol monophosphatase family protein (AHRD V1 **** D7MGB6_ARALY); contains Interpro domain(s) IPR011809 Histidinol-phosphate phosphatase, putative, inositol monophosphatase " Solyc02g083380.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H0E1IEG gene_region:4138787741388191 functional_description:"Unknown Protein (AHRD V1)" Solyc03g025710.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:75014317503380 functional_description:"GCN5-related Nacetyltransferase (AHRD V1 ***- B2IU63_NOSP7); contains Interpro domain(s) IPR000182 GCN5-related Nacetyltransferase " Solyc10g074580.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:57460429-

232

2E-20

195

3E-16

641

7E-68

220

4E-19

290

3E-27

274

2E-25

222

3E-19

395

5E-39

213

3E-18

540

3E-56


881


212

882


240

883


358

884


228

885


156

886


104

887


233

888


215

889


414

57463531 functional_description:"Aminoacylase ACY1 and related metalloexopeptidases (ISS) (AHRD V1 *-*Q00SR9_OSTTA)" Solyc02g063490.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3014232530146879 functional_description:"Malate dehydrogenase (AHRD V1 **** B9S7S1_RICCO); contains Interpro domain(s) IPR010097 Malate dehydrogenase, NADdependent, eukaryotes and gamma proteobacteria " Solyc06g066680.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3828551338288577 functional_description:"Mitochondrial carrier protein (AHRD V1 ***- D2VIZ2_NAEGR); contains Interpro domain(s) IPR002067 Mitochondrial carrier protein " Solyc02g087430.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4445750144459814 functional_description:"Inositol 1 4 5trisphosphate 5-phosphatase-like protein (AHRD V1 **** Q6H453_ORYSJ); contains Interpro domain(s) IPR000300 Inositol polyphosphate related phosphatase " Solyc11g069330.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:5101866751020085 functional_description:"Arabidopsis thaliana genomic DNA chromosome 5 P1 clone MOK16 (AHRD V1 **-- Q9LYW6_ARATH)" Solyc12g055930.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:4727801247281609 functional_description:"UDP-glucose 4epimerase (AHRD V1 ***- Q6XZA0_SOLTU); contains Interpro domain(s) IPR005886 UDP-glucose 4-epimerase " Solyc12g049290.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:4622442046224764 functional_description:"ELF4-like protein (AHRD V1 ***- C6ZKI0_SOLLC); contains Interpro domain(s) IPR009741 Protein of unknown function DUF1313 " Solyc08g041870.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:2749483727499812 functional_description:"Aspartate aminotransferase (AHRD V1 **** Q2XTE6_SOLTU); contains Interpro domain(s) IPR000796 Aspartate/other aminotransferase " Solyc10g076840.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:5913063559138819 functional_description:"1-aminocyclopropane-1carboxylate oxidase 1 (AHRD V1 **-- ACCO1_MALDO); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc08g006470.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:10660491067944 functional_description:"Zinc finger family protein (AHRD V1 ***- D7MB67_ARALY); contains Interpro domain(s) IPR007087 Zinc finger, C2H2-type "

242

1E-21

396

2E-39

608

4E-64

404

2E-40

252

8E-23

171

2E-13

376

4E-37

250

1E-22

622

2E-65



228

891


128

892


469

893


534

894


125

895


526

896


543

897


443

898


128

899


195

Solyc08g006470.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:10660491067944 functional_description:"Zinc finger family protein (AHRD V1 ***- D7MB67_ARALY); contains Interpro domain(s) IPR007087 Zinc finger, C2H2-type " Solyc08g080290.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6077330560774383 functional_description:"Ethylene-responsive transcription factor 1 (AHRD V1 *-** ERF1_ORYSJ); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc04g051360.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H0E1IEG gene_region:4957589949577187 functional_description:"Ethylene responsive transcription factor 2b (AHRD V1 *-*- C0J9I6_9ROSA); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc02g080410.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H0E1IEG gene_region:3921805839218585 functional_description:"class I heat shock protein (AHRD V1 ***- Q69BI7_CARPA); contains Interpro domain(s) IPR008978 HSP20-like chaperone " Solyc02g071490.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3548268935484590 functional_description:"1-aminocyclopropane-1carboxylate oxidase 1 (AHRD V1 **-- ACCO1_MALDO); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc06g065950.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:3772480037727376 functional_description:"Vesicle-associated membrane protein 7C (AHRD V1 **-D7MAR2_ARALY); contains Interpro domain(s) IPR001388 Synaptobrevin " Solyc02g067920.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3258436932589839 functional_description:"Abhydrolase domaincontaining protein FAM108B1 (AHRD V1 *--C0HAS5_SALSA)" Solyc03g059180.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:2523432325242394 functional_description:"Extracellular calcium sensing receptor (AHRD V1 *-*- C7BCU7_LIQFO); contains Interpro domain(s) IPR001763 Rhodanese-like " Solyc04g056340.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5323656853238104 functional_description:"Tyrosine phosphatase family protein (AHRD V1 **** B8N9Z8_ASPFN); contains Interpro domain(s) IPR020428 Protein-tyrosine phosphatase, dual specificity phosphatase, eukaryotic " Solyc08g065320.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5043897450439950 functional_description:"Transmembrane protein 222 (Fragment) (AHRD V1 *--- Q5SSD9_HUMAN);

314

5E-30

227

7E-20

566

6E-59

512

2E-52

213

3E-18

777

3E-83

659

1E-69

717

2E-76

214

2E-18

288

6E-27


900


248

901


233

902


553

903


131

904


246

905


139

906


443

907


183

908


368

909


224

910


96

contains Interpro domain(s) IPR008496 Protein of unknown function DUF778 " Solyc03g007770.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:23193422321665 functional_description:"C4-dicarboxylate transporter/malic acid transport family protein (AHRD V1 **** D7M2F7_ARALY); contains Interpro domain(s) IPR004695 C4-dicarboxylate transporter/malic acid transport protein " Solyc03g006250.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:864358-868678 functional_description:"GDSL esterase/lipase At1g28590 (AHRD V1 **** GDL8_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc08g014150.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:37496133764127 functional_description:"GRAM domain containing protein (AHRD V1 ***- B4FWB9_MAIZE); contains Interpro domain(s) IPR004182 GRAM " Solyc01g090700.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7610010276108119 functional_description:"Enoyl-CoA-hydratase (AHRD V1 ***- Q9SE41_AVIMR); contains Interpro domain(s) IPR001753 Crotonase, core " Solyc08g006150.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:876173-877868 functional_description:"ChaC cation transport regulator-like 1 (AHRD V1 ***- A8KBI8_DANRE); contains Interpro domain(s) IPR006840 ChaC-like protein " Solyc08g006150.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:876173-877868 functional_description:"ChaC cation transport regulator-like 1 (AHRD V1 ***- A8KBI8_DANRE); contains Interpro domain(s) IPR006840 ChaC-like protein " Solyc05g009330.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:34775263482324 functional_description:"COSII_At1g13380 (Fragment) (AHRD V1 *-*- C0KEX8_SOLPN); contains Interpro domain(s) IPR009606 Protein of unknown function DUF1218 " ******* Solyc03g094120.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4932113549322736 functional_description:"Os03g0849800 protein (Fragment) (AHRD V1 *--- Q0DLS4_ORYSJ)" Solyc04g015340.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:55265585531150 functional_description:"Serine carboxypeptidase K10B2.2 (AHRD V1 **** B6TM29_MAIZE); contains Interpro domain(s) IPR001563 Peptidase S10, serine carboxypeptidase " Solyc06g068900.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3910737539108672 functional_description:"Nudix hydrolase 4

416

8E-42

287

7E-27

575

8E-60

225

1E-19

204

3E-17

242

1E-21

426

2E-71

*******

*******

315

5E-30

330

8E-32

169

3E-13


911


516

912


352

913


344

914


322

915


425

916


317

917


305

918


118

919


128

920


132

921


125

(AHRD V1 *-*- B6T5N7_MAIZE); contains Interpro domain(s) IPR000086 NUDIX hydrolase domain " Solyc01g079760.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7141729571424833 functional_description:"Mitochondrial carrier protein (AHRD V1 ***- C5P0Z3_COCP7); contains Interpro domain(s) IPR001993 Mitochondrial substrate carrier " Solyc06g006100.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:11310511137923 functional_description:"Anthranilate synthase component I family protein expressed (AHRD V1 **** Q10B97_ORYSJ); contains Interpro domain(s) IPR005256 Anthranilate synthase component I " Solyc06g071450.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4035128540356266 functional_description:"RNA polymerase II transcription factor B subunit 4 (AHRD V1 **** B6K6N1_SCHJY); contains Interpro domain(s) IPR004600 Transcription factor Tfb4 " Solyc04g008290.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:19747281980067 functional_description:"Microtubule-associated protein MAP65-1a (AHRD V1 **** C0JA45_ORYPU); contains Interpro domain(s) IPR007145 MAP65/ASE1 " Solyc06g065580.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3735863737366698 functional_description:"Uridine kinase (AHRD V1 ***- D7LLX3_ARALY); contains Interpro domain(s) IPR000764 Uridine kinase " Solyc09g005620.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:426287-428915 functional_description:"Glutaredoxin (AHRD V1 *-*D7G070_ECTSI); contains Interpro domain(s) IPR004480 Glutaredoxin-related protein " Solyc02g069240.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3375968333760993 functional_description:"Protein-Ofucosyltransferase 1 (AHRD V1 ***- Q659R8_ORYSA)" Solyc08g006110.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H0E0IEG gene_region:849550-854132 functional_description:"Opaque 2 (Fragment) (AHRD V1 *-- Q84Y96_ZEAMM); contains Interpro domain(s) IPR011616 bZIP transcription factor, bZIP-1 " ******* Solyc09g082720.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6381682263819894 functional_description:"Aldo/keto reductase family protein (AHRD V1 **** D7KWQ9_ARALY); contains Interpro domain(s) IPR001395 Aldo/keto reductase " Solyc08g075750.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5703364157038129 functional_description:"ATP-dependent Clp

736

3E-86

227

7E-20

574

4E-60

532

3E-55

716

2E-76

528

8E-55

306

8E-48

183

8E-15

*******

*******

227

7E-20

202

5E-17


922


59

923


145

924


265

925


242

926


164

927


516

928


341

929


101

930


511

931


133

protease proteolytic subunit (AHRD V1 ***A9PA38_POPTR); contains Interpro domain(s) IPR001907 Peptidase S14, ClpP " ******* Solyc09g075730.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:6284770962851823 functional_description:"Receptor-like kinase (AHRD V1 ***- A7VM37_MARPO); contains Interpro domain(s) IPR013210 Leucine-rich repeat, N-terminal " Solyc02g076810.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3649989736502986 functional_description:"Transcription factor (AHRD V1 *--* D7LW59_ARALY); contains Interpro domain(s) IPR006578 MADF domain " Solyc01g073660.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7027843970284943 functional_description:"Uncharacterized MFStype transporter C19orf28 (AHRD V1 **-CS028_HUMAN); contains Interpro domain(s) IPR016196 Major facilitator superfamily, general substrate transporter " Solyc02g085080.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4266437942666541 functional_description:"Transmembrane protein 53 (AHRD V1 *-*- B5X6E4_SALSA); contains Interpro domain(s) IPR008547 Protein of unknown function DUF829, transmembrane 53 " Solyc07g048060.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E0IEG gene_region:5656570556566220 functional_description:"Auxin-induced proteinlike (AHRD V1 **-- Q6YUI4_ORYSJ); contains Interpro domain(s) IPR007613 Protein of unknown function DUF568, DOMON-like " Solyc02g076870.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:3656165736572422 functional_description:"Potential lipid particle serine esterase (AHRD V1 *--- Q59KL3_CANAL); contains Interpro domain(s) IPR007751 Protein of unknown function DUF676, hydrolase-like " Solyc06g009110.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:30537513057707 functional_description:"Nucellin-like aspartic protease (Fragment) (AHRD V1 **-- Q8L886_MAIZE); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc02g091330.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4723442147243033 functional_description:"C20orf4 homolog (AHRD V1 **-- C0H960_SALSA); contains Interpro domain(s) IPR007946 AAR2 " Solyc01g005760.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:496516-499178 functional_description:"Leucine-rich repeat receptor protein kinase EXS (AHRD V1 **-* EXS_ARATH); contains Interpro domain(s) IPR013210 Leucine-rich repeat, Nterminal "

*******

*******

270

7E-25

414

1E-41

323

5E-31

273

3E-25

837

3E-90

572

6E-60

195

3E-16

855

2E-92

257

2E-23



225

933


133

934


221

935


114

936


563

937


133

938


350

939


162

940


132

941


206

942


230

Solyc06g054250.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3355805233562979 functional_description:"5&apos-nucleotidase surE (AHRD V1 ***- D6YVT2_WADCW); contains Interpro domain(s) IPR002828 Survival protein SurE-like phosphatase/nucleotidase " ******* Solyc08g062970.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:4966381049664229 functional_description:"Glutaredoxin (AHRD V1 ***- B9H2P7_POPTR); contains Interpro domain(s) IPR011905 Glutaredoxin-like, plant II " Solyc01g081440.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7315821673159742 functional_description:"Unknown Protein (AHRD V1); contains Interpro domain(s) IPR010410 Protein of unknown function DUF1005 " Solyc01g066970.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:6767740067677720 functional_description:"Flowering promoting factor-like 1 (Fragment) (AHRD V1 *--A6MZJ6_ORYSI)" Solyc12g010410.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:34570353460558 functional_description:"Homeobox protein knotted-1-like 3 (AHRD V1 ***- B6T3D1_MAIZE); contains Interpro domain(s) IPR005541 KNOX2 " Solyc10g079200.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6010978360110871 functional_description:"Mitochondrial carrier protein (AHRD V1 ***- B1N662_SOLLC); contains Interpro domain(s) IPR018108 Mitochondrial substrate/solute carrier IPR001993 Mitochondrial substrate carrier " Solyc03g031600.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H0E1IEG gene_region:83682458372770 functional_description:"Peroxisomal membrane protein PMP22 (AHRD V1 ***- B6TFH7_MAIZE); contains Interpro domain(s) IPR007248 Mpv17/PMP22 " Solyc08g079110.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5991837659922924 functional_description:"Pentapeptide repeat (AHRD V1 *-*- Q4C7L8_CROWT); contains Interpro domain(s) IPR001646 Pentapeptide repeat " Solyc06g073240.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4152319241524084 functional_description:"Acetyl xylan esterase A (AHRD V1 **-- D7JXX9_9BACE); contains Interpro domain(s) IPR005181 Protein of unknown function DUF303, acetylesterase putative " Solyc10g007320.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:17233621727492 functional_description:"Uroporphyrinogen decarboxylase (AHRD V1 **** D7L387_ARALY);

278

8E-26

*******

*******

362

1E-35

182

1E-14

444

1E-44

218

7E-19

516

2E-53

218

7E-19

219

6E-19

381

9E-38

393

4E-39


943


185

944


136

945


357

946


147

947


321

948


330

949

LesAffx.67948.1.S1_s_at

127

950


464

951


128

contains Interpro domain(s) IPR006361 Uroporphyrinogen decarboxylase HemE " Solyc09g082270.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6345427763455576 functional_description:"Non-specific lipidtransfer protein (AHRD V1 ***- B9SFJ1_RICCO); contains Interpro domain(s) IPR013770 Plant lipid transfer protein and hydrophobic protein, helical " Solyc04g078460.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6077720960778514 functional_description:"N(4)-(Beta-Nacetylglucosaminyl)-L-asparaginase (AHRD V1 **** ASPG_ELIMR); contains Interpro domain(s) IPR000246 Peptidase T2, asparaginase 2 " Solyc03g111180.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5588153555887683 functional_description:"Aspartyl aminopeptidaselike protein (AHRD V1 ***- Q8LF32_ARATH); contains Interpro domain(s) IPR001948 Peptidase M18, aminopeptidase I " Solyc11g008590.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H0E1IEG gene_region:27785932785148 functional_description:"UDP-galactose transporter-like protein (AHRD V1 *-*- O65494_ARATH); contains Interpro domain(s) IPR007271 Nucleotide-sugar transporter " Solyc06g048920.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:2843799128441454 functional_description:"Glycerol-3-phosphate dehydrogenase (AHRD V1 **** A8IKS4_CHLRE); contains Interpro domain(s) IPR006168 NAD-dependent glycerol-3-phosphate dehydrogenase " Solyc02g081510.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E0IEG gene_region:4002020340021557 functional_description:"Receptor-like protein kinase (AHRD V1 **** Q9M576_ORYSA); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase " Solyc03g120500.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:6293125562932952 functional_description:"Auxin responsive protein (AHRD V1 ***- D9IQE6_CATRO); contains Interpro domain(s) IPR003311 AUX/IAA protein " Solyc11g065530.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:4805431248055826 functional_description:"Lipase (Fragment) (AHRD V1 ***- Q9ZTW1_DIACA); contains Interpro domain(s) IPR002921 Lipase, class 3 " Solyc06g076350.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4383060043832729 functional_description:"Transcription factor (Fragment) (AHRD V1 *--* D6MKQ8_9ASPA); contains Interpro domain(s) IPR006447 Myb-like DNA-binding region, SHAQKYF class "

212

5E-23

229

4E-20

631

9E-67

255

4E-23

559

2E-58

489

3E-50

216

1E-18

745

1E-79

213

3E-18



169

953


315

954


473

955


558

956


165

957


332

958


333

959


302

960


219

961


130

Solyc06g050700.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H0E0IEG gene_region:2996209129962401 functional_description:"Early response to dehydration 15-like protein (Fragment) (AHRD V1 **-Q5MEE1_PSEMZ)" Solyc09g014900.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:71561707158366 functional_description:"Cytochrome P450 71 family protein (AHRD V1 ***- C7FGM0_SOLLC); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc08g063080.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:4984157549843854 functional_description:"UDP-sulfoquinovose synthase (AHRD V1 ***- C0LIR3_SOLLC); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc03g080100.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:4555411145556084 functional_description:"Copper-translocating Ptype ATPase (AHRD V1 *--- Q3JHP1_BURP1); contains Interpro domain(s) IPR006121 Heavy metal transport/detoxification protein " Solyc06g071750.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4058753340588181 functional_description:"Octicosapeptide/Phox/Bem1p domain-containing protein (AHRD V1 **-D7LRK8_ARALY); contains Interpro domain(s) IPR000270 Octicosapeptide/Phox/Bem1p " Solyc07g008050.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:27627912767317 functional_description:"RING finger protein (AHRD V1 **-- B6JVU3_SCHJY); contains Interpro domain(s) IPR001607 Zinc finger, UBP-type " Solyc05g052240.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:6165784161660121 functional_description:"Chalcone--flavonone isomerase (AHRD V1 ***- B4G1R6_MAIZE); contains Interpro domain(s) IPR003466 Chalcone isomerase, subgroup " Solyc05g051240.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6066603760667380 functional_description:"Aspartic proteinase nepenthesin I (AHRD V1 ***- A9ZMF9_NEPAL); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc04g015340.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:55265585531150 functional_description:"Serine carboxypeptidase K10B2.2 (AHRD V1 **** B6TM29_MAIZE); contains Interpro domain(s) IPR001563 Peptidase S10, serine carboxypeptidase " Solyc08g068590.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5493350854938841 functional_description:"PAP fibrillin family

333

3E-32

530

5E-55

774

5E-83

536

3E-55

249

2E-22

401

4E-40

506

3E-52

356

7E-35

376

3E-37

206

2E-17


962


394

963


347

964


562

965


351

966


479

967


200

968


401

969


317

970


131

971


427

protein (AHRD V1 ***- B5W0K3_SPIMA); contains Interpro domain(s) IPR006843 PAP fibrillin " Solyc08g066700.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5273128252736672 functional_description:"Polyribonucleotide nucleotidyltransferase (AHRD V1 ***- PNP_PROVI); contains Interpro domain(s) IPR001247 Exoribonuclease, phosphorolytic domain 1 " Solyc12g006060.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H0E1IEG gene_region:648797-656982 functional_description:"Unknown Protein (AHRD V1)" Solyc02g076710.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3641925536421938 functional_description:"Cathepsin B-like cysteine proteinase (AHRD V1 *--* CYSP_SCHMA); contains Interpro domain(s) IPR013128 Peptidase C1A, papain " Solyc06g008760.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H1E1IEG gene_region:26806152680920 functional_description:"Glutaredoxin (AHRD V1 ***- B3F8F2_SOLTU); contains Interpro domain(s) IPR011905 Glutaredoxin-like, plant II " Solyc12g089240.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:6279273662795008 functional_description:"Zinc finger protein CONSTANS-LIKE 3 (AHRD V1 *--- COL3_ARATH); contains Interpro domain(s) IPR000315 Zinc finger, B-box " Solyc08g067260.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5351916953522606 functional_description:"Fatty acid elongase 3ketoacyl-CoA synthase (AHRD V1 **** Q6DUV6_BRANA); contains Interpro domain(s) IPR012392 Very-long-chain 3-ketoacyl-CoA synthase " Solyc04g081930.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6337389863377087 functional_description:"Prolyl 4-hydroxylase alpha-2 subunit (AHRD V1 ***- B6TYA6_MAIZE); contains Interpro domain(s) IPR006620 Prolyl 4hydroxylase, alpha subunit " Solyc06g083380.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:4508848845092545 functional_description:"Acyl-ACP thioesterase (AHRD V1 **** D7RU32_CAPAN); contains Interpro domain(s) IPR002864 Acyl-ACP thioesterase " Solyc12g009610.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:28653282876560 functional_description:"TBC1 domain family member 15 (AHRD V1 *--- Q6P4X9_XENTR); contains Interpro domain(s) IPR000195 RabGAP/TBC " Solyc04g014730.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:49938644999385 functional_description:"Fumarylacetoacetase (AHRD V1 **** Q2HT34_MEDTR); contains Interpro domain(s) IPR005959 Fumarylacetoacetase "

661

4E-70

501

1E-51

829

3E-89

527

1E-54

674

2E-71

327

2E-31

365

9E-36

566

3E-59

211

5E-18

737

8E-79



208

973


313

974


170

975


213

976


443

977


485

978


105

979


325

980


349

981


495

Solyc07g054850.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:6035769660358745 functional_description:"Uncharacterized GPIanchored protein At4g28100 (AHRD V1 ***UGPI7_ARATH)" Solyc12g011160.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:40092684013862 functional_description:"Enoyl-CoA-hydratase (AHRD V1 ***- Q9SE41_AVIMR); contains Interpro domain(s) IPR001753 Crotonase, core " Solyc10g081260.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6171175961714548 functional_description:"Multidrug resistance protein mdtK (AHRD V1 ***- MDTK_ERWAM); contains Interpro domain(s) IPR002528 Multi antimicrobial extrusion protein MatE " Solyc01g080910.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7276051172761503 functional_description:"Unknown Protein (AHRD V1)" Solyc11g056680.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H1E1IEG gene_region:4513928245140376 functional_description:"Leucine-rich repeat family protein / protein kinase family protein (AHRD V1 **-- C6ZRZ7_SOYBN); contains Interpro domain(s) IPR013210 Leucine-rich repeat, N-terminal " Solyc09g011040.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:43835494384838 functional_description:"Aspartic proteinase nepenthesin I (AHRD V1 **-- A9ZMF9_NEPAL); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc07g053480.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:5925308559255344 functional_description:"Ras-related protein Rab25 (AHRD V1 ***- RAB25_BOVIN); contains Interpro domain(s) IPR015595 Rab11-related " Solyc02g083500.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4145333041456369 functional_description:"Genomic DNA chromosome 5 TAC clone K2A18 (AHRD V1 ***Q9FKX3_ARATH); contains Interpro domain(s) IPR006016 UspA " Solyc07g052960.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:5869233158693620 functional_description:"GRAS family transcription factor (AHRD V1 **-* B9MXU3_POPTR); contains Interpro domain(s) IPR005202 GRAS transcription factor " Solyc02g084870.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4251403242516405 functional_description:"Mitogen-activated protein kinase 7 (AHRD V1 ***- D9IV43_SOLLC); contains Interpro domain(s) IPR002290 Serine/threonine protein kinase "

327

2E-31

532

3E-55

295

9E-28

344

2E-33

703

7E-75

739

6E-79

178

3E-14

366

5E-36

594

2E-62

689

2E-87



418

983


351

984


496

985


457

986


454

987


518

988


151

989


111

990


546

991


130

992


356

993


177

Solyc04g072000.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:5665906056660689 functional_description:"Chitinase (AHRD V1 ***- D0QU15_LACSA); contains Interpro domain(s) IPR016283 Glycoside hydrolase, family 19 " Solyc01g099040.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8114217681143761 functional_description:"GDSL esterase/lipase At5g03980 (AHRD V1 **** GDL74_ARATH); contains Interpro domain(s) IPR001087 Lipase, GDSL " Solyc02g087740.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:4463012744632404 functional_description:"Cupin RmlC-type (AHRD V1 **-- B4F886_MAIZE); contains Interpro domain(s) IPR012864 Protein of unknown function DUF1637 " ******* Solyc07g062060.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6211880062121269 functional_description:"Peptide methionine sulfoxide reductase msrB (AHRD V1 ***B6T2N3_MAIZE); contains Interpro domain(s) IPR002579 Methionine sulphoxide reductase B " Solyc07g040710.1.1 genomic_reference:SL2.31ch07 evidence_code:10F0H1E1IEG gene_region:4674112246743116 functional_description:"Calmodulin-binding protein (AHRD V1 **** A2I5F3_BETVU)" Solyc02g071520.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3549517335497914 functional_description:"RAG1-activating protein 1 homolog (AHRD V1 **-- R1AP1_DICDI); contains Interpro domain(s) IPR018179 RAG1-activating protein 1 homologue " Solyc09g008460.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:19059141910904 functional_description:"Ras-related protein Rab-18 (AHRD V1 ***- B6TSE5_MAIZE); contains Interpro domain(s) IPR015598 Rab18 " Solyc03g113280.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:5751757457522333 functional_description:"Membrane protein HPP family (AHRD V1 *-*- D9Y9E6_9DELT); contains Interpro domain(s) IPR007065 HPP " Solyc12g088880.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:6252410162527732 functional_description:"Epimerase/dehydratase (AHRD V1 ***- C7JBC7_ACEP3); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc10g078430.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:5957045459578711 functional_description:"Transcription factor Dp-1 (AHRD V1 **** B6UDG0_MAIZE); contains Interpro domain(s) IPR016556 Transcription factor DP, subgroup " Solyc02g087150.1.1 genomic_reference:SL2.31ch02

773

5E-83

530

5E-55

490

4E-87

*******

*******

281

1E-48

780

1E-83

248

2E-22

178

3E-14

756

8E-81

231

2E-20

603

2E-63

286

9E-27


994


124

995


408

996


571

997


116

998


126

999


502

1000


470

1001


464

1002


518

1003


401

evidence_code:10F1H0E1IEG gene_region:4422226244225033 functional_description:"Heavy-metal-associated domain-containing protein (AHRD V1 *-*D7M6P1_ARALY); contains Interpro domain(s) IPR006121 Heavy metal transport/detoxification protein " ******* Solyc10g052490.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:4829050148292118 functional_description:"Isoflavone reductase-like protein 5 (AHRD V1 ***- Q3KN68_VITVI); contains Interpro domain(s) IPR008030 NmrA-like " Solyc11g066820.1.1 genomic_reference:SL2.31ch11 evidence_code:10F1H1E1IEG gene_region:4971109949718621 functional_description:"Cellulose synthase-like C6 glycosyltransferase family 2 (AHRD V1 **-A6N4C3_PHYPA); contains Interpro domain(s) IPR001173 Glycosyl transferase, family 2 " Solyc06g009270.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:32267453236416 functional_description:"Diacylglycerol kinase 7 (AHRD V1 **** B0KYU1_ARATH); contains Interpro domain(s) IPR016961 Diacylglycerol kinase, plant " Solyc05g015490.1.1 genomic_reference:SL2.31ch05 evidence_code:10F1H1E1IEG gene_region:1070216510704597 functional_description:"Non-specific lipidtransfer protein (AHRD V1 ***- Q700A6_CICAR); contains Interpro domain(s) IPR003612 Plant lipid transfer protein/seed storage/trypsin-alpha amylase inhibitor " Solyc01g079940.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7160629171608196 functional_description:"Xylanase inhibitor (Fragment) (AHRD V1 **-- Q53IQ4_WHEAT); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc01g079200.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7079419870797188 functional_description:"Gibberellin 2-oxidase (AHRD V1 **** A4GVL7_SOLLC); contains Interpro domain(s) IPR005123 Oxoglutarate and iron-dependent oxygenase " Solyc02g081400.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3996309839967114 functional_description:"Intracellular protease PfpI family protein expressed (AHRD V1 ***Q2R1V5_ORYSJ); contains Interpro domain(s) IPR006286 Peptidase C56, PfpI " Solyc01g108240.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8736862987369516 functional_description:"Ethylene responsive transcription factor 2b (AHRD V1 *-*- C0J9I6_9ROSA); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc05g054570.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6360582863611388 functional_description:"CRAL/TRIO domain

*******

*******

551

6E-62

990

1E-108

219

6E-19

230

3E-20

842

7E-91

792

4E-85

807

7E-87

476

2E-48

714

3E-76


1004


133

1005


522

1006


129

1007


131

1008


132

1009


485

1010


414

1011


133

1012


258

1013


129

containing protein expressed (AHRD V1 **-Q84TA5_ORYSJ); contains Interpro domain(s) IPR001251 Cellular retinaldehyde-binding/triple function, C-terminal " Solyc01g007220.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:18010111801646 functional_description:"NHL1 (Fragment) (AHRD V1 **-- B0LZM3_ARATH); contains Interpro domain(s) IPR010847 Harpin-induced 1 " Solyc03g044900.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:1474741014748110 functional_description:"Calmodulin-like protein 41 (AHRD V1 ***- B6T5H7_MAIZE); contains Interpro domain(s) IPR011992 EF-Hand type " Solyc08g067050.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5317159753177354 functional_description:"Arginine Nmethyltransferase family protein (AHRD V1 ***D7KE86_ARALY); contains Interpro domain(s) IPR010456 Ribosomal L11 methyltransferase " Solyc02g084960.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H0E1IEG gene_region:4257255042573299 functional_description:"Genomic DNA chromosome 5 TAC clone K1F13 (AHRD V1 ***Q9FJZ5_ARATH)" Solyc04g009810.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:31177683125507 functional_description:"Pelota homolog (AHRD V1 ***- C3KIY5_ANOFI); contains Interpro domain(s) IPR004405 Probable translation factor pelota " Solyc01g010200.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H0E1IEG gene_region:49886334989181 functional_description:"LTRGag-pol-polymerase 3 (AHRD V1 ***- B2BXJ4_ARALY)" Solyc07g063960.1.1 genomic_reference:SL2.31ch07 evidence_code:10F1H1E1IEG gene_region:6351985963522329 functional_description:"50S ribosomal protein L24 (AHRD V1 ***- B4FTJ3_MAIZE); contains Interpro domain(s) IPR003256 Ribosomal protein L24 " Solyc06g083690.1.1 genomic_reference:SL2.31ch06 evidence_code:10F1H0E1IEG gene_region:4531869045322933 functional_description:"Glutaredoxin (AHRD V1 *-*- B5A8A6_WHEAT); contains Interpro domain(s) IPR011899 Glutaredoxin, eukaryotic and viruses " Solyc03g083960.1.1 genomic_reference:SL2.31ch03 evidence_code:10F1H1E1IEG gene_region:4744320447445217 functional_description:"Trehalose 6-phosphate phosphatase (AHRD V1 **** D4QAK5_TOBAC); contains Interpro domain(s) IPR003337 Trehalose-phosphatase " Solyc08g082170.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6219637762200475 functional_description:"Glycoside hydrolase family 28 protein/polygalacturonase family protein (AHRD V1 **-- Q1PF10_ARATH); contains Interpro domain(s) IPR012334 Pectin lyase fold "

193

6E-16

703

1E-74

203

4E-17

216

1E-18

224

1E-19

702

1E-74

520

1E-53

219

6E-19

446

3E-45

229

4E-20



275

1015


207

1016


263

1017


113

1018


384

1019


145

1020


129

1021


507

1022


276

1023


95

Solyc01g079590.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:7120597271213117 functional_description:"Transmembrane protein 205 (AHRD V1 ***- B9EN72_SALSA)" Solyc09g072560.1.1 genomic_reference:SL2.31ch09 evidence_code:10F1H1E1IEG gene_region:6059383360595659 functional_description:"Legumin 11S-globulin (AHRD V1 **-- Q39770_GINBI); contains Interpro domain(s) IPR014710 RmlC-like jelly roll fold " Solyc10g006510.1.1 genomic_reference:SL2.31ch10 evidence_code:10F1H1E1IEG gene_region:10869181090437 functional_description:"Transcription factor (Fragment) (AHRD V1 **** D6MKL1_9ASPA); contains Interpro domain(s) IPR011598 Helix-loop-helix DNAbinding " Solyc04g009840.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H0E0IEG gene_region:31634773167475 functional_description:"C-Myc-binding protein (AHRD V1 ***- B4FK57_MAIZE)" Solyc12g005180.1.1 genomic_reference:SL2.31ch12 evidence_code:10F0H1E1IEG gene_region:124158-127837 functional_description:"Chloroplast lipocalin (AHRD V1 ***- Q38JB4_SOLTU); contains Interpro domain(s) IPR013208 Lipocalin-like " Solyc05g055940.1.1 genomic_reference:SL2.31ch05 evidence_code:10F0H1E1IEG gene_region:6452234464525549 functional_description:"Myb family transcription factor (AHRD V1 **-* D7M706_ARALY); contains Interpro domain(s) IPR006447 Myb-like DNA-binding region, SHAQKYF class " Solyc06g054630.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E1IEG gene_region:3384654333847256 functional_description:"Ethylene-responsive transcription factor 1 (AHRD V1 *-*- ERF1_ORYSJ); contains Interpro domain(s) IPR001471 Pathogenesisrelated transcriptional factor and ERF, DNA-binding " Solyc10g052880.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:4956446149565897 functional_description:"Leucine-rich repeat family protein (AHRD V1 **-- Q4PT10_ARATH); contains Interpro domain(s) IPR013210 Leucine-rich repeat, Nterminal " Solyc08g067100.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:5322039653223899 functional_description:"Aspartic proteinase nepenthesin-1 (AHRD V1 **-- C0JA51_9ORYZ); contains Interpro domain(s) IPR001461 Peptidase A1 " Solyc01g106060.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8580378785806771 functional_description:"Glutamine amidotransferase class-I (AHRD V1 **-A2Q1P2_MEDTR); contains Interpro domain(s) IPR000991 Glutamine amidotransferase class-I, C-terminal "

252

8E-23

351

3E-34

420

3E-42

160

4E-12

658

8E-70

242

1E-21

228

5E-20

867

9E-94

477

7E-49

174

9E-14



535

1025


416

1026


323

1027


377

1028

LesAffx.805.1.S1_at

349

1029


111

1030


402

1031


190

1032


220

1033

LesAffx.885.1.S1_at

119

Solyc04g080290.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6212218362124610 functional_description:"CRAL/TRIO domain containing protein expressed (AHRD V1 **-Q75GU9_ORYSJ); contains Interpro domain(s) IPR001251 Cellular retinaldehyde-binding/triple function, C-terminal " Solyc11g021150.1.1 genomic_reference:SL2.31ch11 evidence_code:10F0H0E0IEG gene_region:1337211413373403 functional_description:"Unknown Protein (AHRD V1)" Solyc02g068700.1.1 genomic_reference:SL2.31ch02 evidence_code:10F1H1E1IEG gene_region:3321033133213586 functional_description:"Histidine triad (HIT) protein (AHRD V1 **-- Q2MGQ9_MEDTR); contains Interpro domain(s) IPR001310 Histidine triad (HIT) protein " Solyc08g068330.1.1 genomic_reference:SL2.31ch08 evidence_code:10F1H1E1IEG gene_region:5463696354644818 functional_description:"Aspartate aminotransferase (AHRD V1 **** B9H920_POPTR); contains Interpro domain(s) IPR000796 Aspartate/other aminotransferase " Solyc01g079610.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:7122467071230105 functional_description:"DNAJ chaperone (AHRD V1 ***- B0W7V8_CULQU); contains Interpro domain(s) IPR003095 Heat shock protein DnaJ " Solyc09g057870.1.1 genomic_reference:SL2.31ch09 evidence_code:10F0H1E1IEG gene_region:4716128447162972 functional_description:"Protein FAR1RELATED SEQUENCE 5 (AHRD V1 **-FRS5_ARATH); contains Interpro domain(s) IPR004330 Transcription factor, FAR1-related " Solyc10g083700.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E1IEG gene_region:6279012662793473 functional_description:"Cytochrome P450 (AHRD V1 ***- Q8H0I7_PETHY); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc03g098010.1.1 genomic_reference:SL2.31ch03 evidence_code:10F0H1E1IEG gene_region:5380951153811760 functional_description:"Acid phosphatase (AHRD V1 **** B9XQU4_9BACT); contains Interpro domain(s) IPR004843 Metallophosphoesterase " Solyc02g094400.1.1 genomic_reference:SL2.31ch02 evidence_code:10F0H1E1IEG gene_region:4951366149515281 functional_description:"Glycerophosphodiester phosphodiesterase gde1 (AHRD V1 ***B6JW52_SCHJY); contains Interpro domain(s) IPR004129 Glycerophosphoryl diester phosphodiesterase " Solyc08g080730.1.1 genomic_reference:SL2.31ch08 evidence_code:10F0H1E1IEG gene_region:6110523361110020 functional_description:"Senescence-associated protein (AHRD V1 ***- B3TLS7_ELAGV); contains Interpro domain(s) IPR000301 Tetraspanin, subgroup "

765

7E-82

250

2E-22

410

4E-41

645

3E-68

618

3E-65

195

3E-16

439

2E-44

337

1E-32

357

5E-35

227

7E-20



521

1035


467

1036


493

1037


130

1038


434

1039


555

1040


246

1041


384

Solyc06g035520.1.1 genomic_reference:SL2.31ch06 evidence_code:10F0H1E0IEG gene_region:2112869921130044 functional_description:"Acetyl esterase (AHRD V1 *--- AES_SALSV); contains Interpro domain(s) IPR013094 Alpha/beta hydrolase fold-3 " Solyc01g103590.1.1 genomic_reference:SL2.31ch01 evidence_code:10F1H1E1IEG gene_region:8392942983930271 functional_description:"Glyoxalase/bleomycin resistance protein/dioxygenase (AHRD V1 **-Q2HVV5_MEDTR); contains Interpro domain(s) IPR004360 Glyoxalase/bleomycin resistance protein/dioxygenase " Solyc12g006460.1.1 genomic_reference:SL2.31ch12 evidence_code:10F1H1E1IEG gene_region:935249-939941 functional_description:"Cytochrome P450 (AHRD V1 ***Q9LKH7_9FABA); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc04g078290.1.1 genomic_reference:SL2.31ch04 evidence_code:10F0H1E1IEG gene_region:6064147260644332 functional_description:"Cytochrome P450 (AHRD V1 ***- B9NFM5_POPTR); contains Interpro domain(s) IPR002401 Cytochrome P450, E-class, group I " Solyc10g085920.1.1 genomic_reference:SL2.31ch10 evidence_code:10F0H1E0IEG gene_region:6425829464263075 functional_description:"Bifunctional polymyxin resistance protein ArnA (AHRD V1 **-- ARNA_KLEP3); contains Interpro domain(s) IPR016040 NAD(P)-binding domain " Solyc01g058720.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H0E1IEG gene_region:6082223160822766 functional_description:"NaCl-inducible Ca2+binding protein (AHRD V1 **-* O22368_ARATH); contains Interpro domain(s) IPR011992 EF-Hand type " Solyc01g098550.1.1 genomic_reference:SL2.31ch01 evidence_code:10F0H1E1IEG gene_region:8079747880803182 functional_description:"Tryptophan synthase alpha chain (AHRD V1 ***- Q8LA83_ARATH); contains Interpro domain(s) IPR002028 Tryptophan synthase, alpha chain " Solyc04g081530.1.1 genomic_reference:SL2.31ch04 evidence_code:10F1H1E1IEG gene_region:6306927363069740 functional_description:"Chaperone protein dnaJ 11 (AHRD V1 *-*- B6SUM8_MAIZE); contains Interpro domain(s) IPR001623 Heat shock protein DnaJ, N-terminal "

558

7E-58

655

3E-69

818

4E-88

231

2E-20

700

2E-74

578

4E-60

410

4E-41

538

7E-56

Table S2 List of cell wall modification related genes which showed down-regulation in rin mutant when compared to wild type. Probe Set ID

GenBank/Unigene ID

Les.3654.1.S1_at Les.4463.1.S1_s_at LesAffx.71442.2.S1_at Les.4449.1.S1_s_at Les.5579.1.S1_at Les.3122.2.A1_a_at Les.3630.1.S1_at Les.5233.1.S1_at

X04583.1/Les.4463 M20269.1/Les.17635 BG125039/Les.11646 AY034075.1/Les.268 BT014190.1/Les.5579 S66607.1/Les.3122 U50985.1/Les.3630 CN384566/Les.5233

Target description

Polygalacturonase-2a (PG-2a) Polygalacturonase (PG) Polygalacturonase homologue to AT4G23820 Mannan endo-1,4-beta-mannosidase (Man4) Pectate lyase homologue to AT4G13710 Pectin methylesterase Pectin methylesterase Pectinesterase homologue to ATPME1 (AT1G53840) Les.3979.1.S1_at AF023847.2/Les.3979 Beta-galactosidase (TBG1) Les.1.1.S1_at AF154421.1 /Les.1 Beta-galactosidase (TBG3) Les.4346.1.S1_at AF020390.2/Les.4346 Beta-galactosidase (TBG4) Les.3991.1.S1_at BG627309/Les.3991 Beta-D-xylosidase (LEXYL2) Les.4445.1.S1_at AB041811.1/Les.4445 Beta-D-xylosidase (LEXYL1) Les.4530.1.S1_at AY497479.1/Les.4530 Xyloglucan endotransglucosylase/hydrolase (XTH9) Les.4008.1.S1_a_at BG630151/Les.20919 Xyloglucan endotransglycosylase/hydrolase (XTH16) Les.3461.1.S1_at AJ272304.2/Les.3461 Beta-fructofuranosidase (lin5) Les.1847.2.S1_at BM410423/Les.1847 Beta-glucosidase homologue to AT3G47000 Les.3568.1.S1_at AF059490.1/Les.1741 Expansin (EXPA6) Les.191.1.S1_at AF548376.1/Les.191 Expansin 1 (LeEXP1) Les.3747.1.S1_at Z46675.1/Les.3747 Extensin (Lemmi11) Les.3666.1.S1_at U13055.1/Les.3666 Endo-1,4-beta-glucanase precursor (cel2) Les.5817.1.S1_at AJ785525/Les.5817 Endo-beta-1,4-D-glucanase homologue to ATGH9B5 (AT1G19940) Les.3652.1.S1_at BG631079/Les.3652 Beta(1,3)glucanase, TomQ'b (X74906.1) * Fold expression in rin mutant compared to wild type.

Fold expression* BR -51.1 -4.7 1.9 -8.3 -1.6 1.2 1.4 -3.7

BR+3 -334.2 -59.8 -10.4 -104.3 -39.5 -21.0 -22.3 -3.2

-2.5 -2.7 -7.4 -2.1 1 -7.7 -5.6

-2.5 -3.4 -21.4 -9.2 -7.2 -6.8 1.1

-1 -1.5 -1.2 3 2.3 1 4.5

-4.0 -6.5 -4.1 -3.7 -3.0 -69.4 -5.3

-5.1

16.6

Table S3 List of hormone biosynthesis and signalling related genes differentially expressed between wild type and rin mutant fruits. Probe Set ID

GenBank/Unigene ID

Target description

Fold expression* BR

BR+3

Ethylene Les.3662.1.S1_at

M34289.1/Les.3662

ACC synthase (ACS2)

-1.3

-24.9

Les.3661.1.S1_at

M63490.1/Les.21920

ACC synthase (ACS4)

-2.4

-18.8

Les.3475.1.S1_at

AF179247.1/Les.3475

ACC synthase (ACS8)

1

-5.3

Les.3642.1.S1_at

U17972.1/Les.3642

ACC synthase (LE-ACS3)

-3.4

-4.4

Les.1841.1.S1_at

U72389.1/Les.1841

ACC synthase (LeACS1A)

-1

-2.0

Les.221.1.S1_at

AB013101.1/Les.221

ACC oxidase (LE-ACO4)

2.7

2.1

Les.5917.1.S1_at

AJ715790.1/Les.5917

ACC oxidase (ACO5)

-18.5

-5.2

Les.132.1.S1_at

X58885.1/Les.132

ACC oxidase (ACO4)

-3.2

1.3

Les.3627.1.S1_at

AF004914.1/Les.3627

ACC oxidase (E8)

1.8

-2.7

Les.35.1.S1_at

AF118844.1/Les.35

Ethylene receptor (ETR5)

-1.1

2.7

Les.3500.1.S1_at

AF043085.1/Les.3500


-3.5

-1.3

Les.85.1.S1_at

U38666.1/Les.85

Ethylene receptor (Nr)

-1.4

-1.8

Les.3465.1.S1_at

AY079426.1 /Les.3465


-2.8

-1.9


BE461119/Les.13750

Tomato green ripe-like 1

-1.6

-2.7


BM412032/Les.7905

Cystathionine beta-lyase

-1

-2.2

Les.3766.1.S1_at

U77719.1/Les.3766

-3.3

-1.5


AW033835/Les.11301

-1.3

-2.7


AI898830/Les.10466

-1.4

-2.5

Les.5287.1.S1_at

BT013640.1/Les.5287

2.8

4.9


BG129227/Les.6456

-3.6

-3.6


BI421189/Les.8427

-2.5

-5.6


AI484721/Les.10290

-1.8

-4.3

Les.876.1.A1_at

BG627344/Les.21612

2.8

3.3

Les.4140.1.S1_at

AY192367.1/Les.4140

-3.3

-1.7

Les.3679.1.S1_at

AY044236.1/Les.3679

Ethylene responsive late embryogenesis-like protein (ER5) AP2/ERF transcription factor homologue to At1g63040 AP2/ERF transcription factor homologue to AT5G21960 AP2/ERF transcription factor homologue to APETALA 2 (AT4G36920) AP2/ERF transcription factor homologue to DREB1A (AT4G25480) AP2/ERF transcription factor homologue to RRTF1 (AT4G34410) AP2/ERF transcription factor homologue to ABR1 (AT5G64750) AP2/ERF transcription factor homologue to ATERF1 (AT3G23240) AP2/ERF transcription factor homologue to ATERF2 (AT5G47220) Ethylene-responsive factor (ERF1)

3.1

2.2

Les.4102.1.S1_at

AY192368.1/Les.4102

Ethylene response factor (ERF2)

-2

-3.2

Les.3574.1.S1_at

U89257.1/Les.3574

1

5.4

Les.3985.1.S1_at

AF500011.1 /Les.3985

4.4

-1.8

Les.3575.1.S1_at

U89256.1/Les.3575

AP2/ERF transcription factor homologue to CRF4 (AT4G27950) Dehydration responsive element binding protein (DREB1) AP2/ERF transcription factor homologue to ATERF1 (AT3G23240)

-2.9

1.8

Abscisic acid LesAffx.3253.2.S1_at

AW034203/Les.8152

Abscisic acid 8'-hydroxylase (CYP707A3)

-5.3

-14.4


CK715113/Les.21883

1.5

2.5

Les.582.1.A1_at

BG628493/Les.582

-2.9

-7.9

Les.2810.2.S1_at

BE432004/Les.10075

1.2

-3.4


CN385777

-3.5

-1.7


BE431791/ Les.7959

Abscisic acid receptor homologue to PYL9 (AT1G01360) Serine/threonine phosphatase homologue to AHG1 (At5g51760) Homologue to tetratricopeptide repeat (TPR)-like superfamily protein (AT4G28080) Zinc finger protein (SAP11) homologue to PMZ (AT3G28210) Zinc finger protein homologue to XERICO

-3.5

-1.2

Table S3 List of hormone biosynthesis and signalling related genes differentially expressed between wild type and rin mutant fruits.

(AT2G04240) LesAffx.65922.1.S1_at

AI637288/Les.8391


AW036551/Les.5995

Homologue to REGULATORY COMPONENTS OF ABA RECEPTOR 10 PYL4 (AT2G38310) Cruciferin homologue to ATCRA1 (AT5G44120)

-1.2

-3.1

14.1

-4.5

1.2

-14.1

-2.3

-3.4

2.2

4.4

2.7

-1.8

8.8

6.5

-4.2

-2.1

Gibberillin Les.827.1.S1_at

BG626882/Les.20210

Les.4766.1.S1_at

CN385384/Les.19203

Les.417.1.S1_at

BG629973/Les.417

Les.3625.1.S1_at

L22188.1/Les.13734

LesAffx.344.2.S1_at

AI772989/Les.10420


AW030757/Les.11125

Gibberellin-regulated family protein homologue to At2g30810 Gibberellin-responsive protein homologue to GASA2 (At4g09610) Gibberellin-regulated family protein homologue to At5g59845 Tomato RSI-1 homologue to gibberellin-regulated protein 5 (AT3G02885) Gibberellin-responsive protein homologue to GASA1 (At1g75750) Gibberellin 2-oxidase (SlGA2OX3)

Les.63.1.S1_at

AF049900.1/Les.63

Gibberellin 20-oxidase (20OX-3)

-2.8

1.2


AW625117/Les.10316

1.2

2.5


CN385056/Les.12924

Gibberellin receptor homologue to AtGID1C (At5g27320) Homologue to ATFPF1 (AT5G24860)

3.7

2.8

Les.1495.1.S1_at

BG626098/Les.19325

Myb transcription factor (GAMyb-like1)

3.2

5.2


BI930643/Les.19026

Ent-kaurenoic acidhydrolase homologue to ATKAO2 (AT2G32440)

16.0

-1.1

Les.2668.1.S1_at

AW224185/Les.2668

-1.4

-7.2

Les.5177.1.S1_at

BT013446.1/Les.5177

-1.2

-5.0


AW623752/Les.22986

-1.2

-4.2

LesAffx.67948.1.S1_s_at

BE458482/Les.21895

Indole-3-acetic acid amido synthetase homologue to GH3.3 (At2g23170) Indole-3-acetic acid-amido synthetase homologue to GH3.1 (AT2G14960) SAUR-like auxin-responsive protein homologue to AT1G75590 Auxin-responsive protein (IAA6)

1.3

2.6

Les.3702.1.A1_at

AJ785373/Les.3702

Auxin-regulated (IAA10)

3.9

-1.1

Les.3563.1.S1_at

BM412865/Les.3563

ER auxin binding protein 1 (ERABP1)

-2.7

-3.2

Les.3164.1.A1_at

BG626945/Les.3164

1.4

2.7

Les.5146.1.S1_at

BT013382.1/Les.5146

3.2

3.2

Les.3502.1.S1_at

AF332960.1/Les.3502

-2.5

-1


CN385868

BTB and TAZ domain protein homologue to BT1 (AT5G63160) SAUR-like auxin-responsive protein homologue to AT1G75590 Auxin-regulated dual specificity cytosolic kinase homologue to RIPK (AT2G05940) Auxin-responsive protein (AT5G47530)


AW036686/Les.18167

homologue to dormancy/auxin associated protein [Oryza sativa Japonica Group] NP_001050075.2

Les.3645.1.S1_at Les.2474.2.A1_at

U54770.1/Les.4443 BG735266/Les.19437

-2.2 19.4

-5.0 -1.0

Les.317.1.S1_at

BG631306/Les.317

3.9

1.7

Les.5832.1.S1_at

BT014414.1/Les.5832

6-Deoxocastasterone oxidase (DWARF) Sterol reductase homologue to DIMINUTO 1 (AT3G19820) Cytochrome P450 monooxygenase homologue to CABBAGE3 (AT5G05690) UDP-glucosyltransferase homologue to DOGT1 (AT2G36800)

4.2

4.5

Jasmonic acid carboxyl methyltransferase homologue to JMT (AT1G19640 ) Cystathionine beta-synthase homologue to LEJ2 (AT4G36910) Jasmonate ZIM domain-containing protein homologue to JAZ8 (AT1G30135) Homologue to JASMONATE-ZIM-DOMAIN PROTEIN 3 (AT3G17860)

-4.3

1.7

-1.5

-2.5

-5.4

-4.0

3.6

-2.2

Auxin

-3.1

1.6 1.1

-2.6

Brassinosteroid

Jasmonic acid Les.2504.1.A1_at

BG628687/Les.21075

Les.5628.1.S1_at

BT014280/Les.5628


CN384615


AW621549/Les.12794

Table S3 List of hormone biosynthesis and signalling related genes differentially expressed between wild type and rin mutant fruits.

Les.3140.3.S1_at

BI930800/Les.2747

Les.13.1.S1_at

AJ271093.1/Les.13

3-Ketoacyl-CoA thiolase homologue to KAT2/PED1 (AT2G33150) Allene oxide synthase homologue to DDE2 (AT5G42650)

-3.1

3.1

-2.2

-3.5

Homologue to SUPPRESSOR OF SALICYLIC ACID INSENSITIVITY 1 (AT5G24300 ) Methyl esterase homologue to ATMES1 (AT2G23620) Methyl esterase homologue to ATMES1 (AT2G23620) Methyl esterase homologue to ATMES1 (AT2G23620)

-1.1

-3.6

1.4

-14.4

1.8

-8.1

1.2

-3.9

4.6

-1.1

Salicylic acid Les.4890.1.S1_at

BM410663/Les.4890


BI928709/Les.12190


CD002272/Les.10796


AW621893/Les.12886

Cytokinin LesAffx.58244.1.S1_at

BG642575/Les.8802

Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG6 (NP_001244911.1) * Fold expression in rin mutant compared to wild type.

Table S4 List of transcription factors differentially expressed between wild type and rin mutant fruits. Probe Set ID

GenBank/Unigene ID

Target description

Fold expression* BR

BR+3

AP2/ERF LesAffx.63544.1.S1_at

AW033835/Les.11301

AP2/ERF transcription factor homologue to At1g63040

-1.3

-2.7


AI898830/Les.10466

AP2/ERF transcription factor homologue to AT5G21960

-1.4

-2.5

Les.5287.1.S1_at

BT013640.1/Les.5287

2.8

4.9


BG129227/Les.6456

-3.6

-3.6


BI421189/Les.8427

-2.5

-5.6


AI484721/Les.10290

-1.8

-4.3

Les.876.1.A1_at

BG627344/Les.21612

2.8

3.3

Les.4140.1.S1_at

AY192367.1/Les.4140

-3.3

-1.7

Les.3679.1.S1_at

AY044236.1/Les.3679

AP2/ERF transcription factor homologue to APETALA 2 (AT4G36920) AP2/ERF transcription factor homologue to DREB1A (AT4G25480) AP2/ERF transcription factor homologue to RRTF1 (AT4G34410) AP2/ERF transcription factor homologue to ABR1 (AT5G64750) AP2/ERF transcription factor homologue to ATERF1 (AT3G23240) AP2/ERF transcription factor homologue to ATERF2 (AT5G47220) Ethylene-responsive factor (ERF1)

3.1

2.2

Les.4102.1.S1_at

AY192368.1/Les.4102

Ethylene response factor (ERF2)

-2

-3.2

Les.3574.1.S1_at

U89257.1/Les.3574

1

5.4

Les.3985.1.S1_at

AF500011.1/Les.3985

AP2/ERF transcription factor homologue to CRF4 (AT4G27950) Dehydration responsive element binding protein (DREB1)

4.4

-1.8

Les.3575.1.S1_at

U89256.1/Les.3575

AP2/ERF transcription factor homologue to ATERF1 (AT3G23240)

-2.9

1.8


BE459012/Les.22349

Myb transcription factor homologue to PCL1 (AT3G46640)

-1.1

-2.6

Les.2886.2.S1_at

AW934438/Les.2886

Myb transcription factor homologue to RVE2 (AT5G37260)

1.7

-2.5


AI771347/Les.10272

Myb transcription factor homologue to PHL1 (AT5G29000)

2

2.8

Les.17.1.S1_at

X99134.1/Les.17

Myb-related transcription factor (THM6)

-1

3.3

Les.1495.1.S1_at

BG626098/Les.19325

Myb transcription factor (GAMyb-like1)

3.2

5.2

Les.4923.1.S1_at

BT012912.1/Les.4923

3

2.6

Les.5017.1.A1_at

BT013110.1/Les.5017

2.6

1.2


BI922753/Les.11552

-1.5

-2.6

Les.1314.1.S1_at

BG630759/Les.8142

Myb-related transcription factor homologue to ATCCA1 (AT2G46830) Myb family transcription factor homologue to ATMYB 48 (AT3G46130) Myb transcription factor homologue to ATMYB96 (AT5G62470) Myb family transcription factor homologue to RVE1 (AT5G17300)

3.8

2.1

MYB

WRKY Les.3962.1.A1_at

BG630092/Les.3962

WRKY transcription factor IId-3 (WRKYIId-3)

-1

3.6

Les.5102.1.S1_at

BT013284.1/Les.5102

-1

3.8

Les.3964.1.S1_at

AY157060.1/Les.3964

WRKY transcription factor homologue to ATWRKY65 (AT1G29280) WRKY transcription factor IId-2 (WRKYIId-2)


BE435747/Les.12719

Les.5226.1.S1_at

BT013530.1/Les.5226

-2.8

-1.3

WRKY transcription factor homologue to ATWRKY6 (AT1G62300) WRKY transcription factor homologue to ATWRKY20 (AT4G26640)

-2.7

-1.6

-1.3

2.9

-1.3

-3.5

2

2.6

1.3

2.8

NAC Les.288.1.S1_at

BM410927/Les.15620

NAC transcription factor (NAC-NOR)

Les.5820.1.S1_at

BT014626.1/Les.5820

Les.323.1.S1_at

Z75524.1/Les.13895

NAC transcription factor homologue to ANAC050 (AT3G10480) NAC transcription factor homologue to ANAC083 (AT5G13180)

bHLH

Les.1376.2.A1_at

BG629093/Les.1376

bHLH transcription factor homologue to GL3 (AT5G41315)

3

1.8

Les.5638.1.S1_at

BT014300.1/Les.5638

1.4

-4.2

Les.4085.1.S1_at

BE459897/Les.4085

bHLH transcription factor homologue to CIB1 (AT4G34530 ) bHLH transcription factor LHW (AT2G27230)

2.9

2.3


BF050476/Les.12882

bHLH transcription factor homologue to ILR3 (AT5G54680)

-3.3

1.4


BI926331/Les.5999

3.4

2.7


AI781951/Les.11268

3.9

5.3


BI923284/Les.16962

B-box type zinc finger transcription factor homologue to (AT4G27310) C2H2 type zinc finger transcription factor homologue to AT4G31420 CONSTANS 1 homologue to ATCOL1 (AT5G15850)

2.8

2.1

Les.2921.1.S1_at

BT013260.1/Les.2921

1.3

2.5


BF051890/Les.6805

B-box type zinc finger transcription factor homologue to (ATCOL4) AT5G24930 Zinc finger (B-box type) family protein (AT5G48250)

2.8

-1.2

Les.681.1.A1_at

BG626881/Les.681

Zinc finger (C2H2 type) family ZFP4 (AT1G66140)

3.5

-1.0


CK715035

-1.6

4.3

LesAffx.109.1.A1_at

AI780243

1.2

4.4


BM411685/Les.12667

Zinc finger (B-box type) family protein homologue to ATCOL4 (AT5G24930) C2H2-like zinc finger protein homologue to IDD1 ( AT5G66730) B-box zinc finger family protein homologue to AT4G39070

-1.5

-3.7

BT014057.1/Les.1967 4 AY306154.1/Les.4362

MADS-box transcription factor (LeFUL2)

-1.7

-2.6

AF448522.1/Les.1834 9 AF448523.1/Les.1924 8 BI932334/Les.9196

MADS-box transcription factor MADS-RIN

Zinc finger

MADS-box Les.4339.1.S1_at Les.4362.1.A1_at

3.1

8.2

-30.3

-90

MADS-box transcription factor MADS-rin /// MADS-box transcription factor MADS-MC MADS box transcription factor homologue to AGL11 (AT4G09960)

2.6

8.2

3.7

2.2

BT013474.1/Les.1769 6 BM536341/Les.12668

GRAS (scarecrow) transcription factor homologue to AT5G66770 GRAS (scarecrow) transcription factor homologue to AT3G49950

-1.4

3.0

-1.8

-4.7

Les.4889.1.S1_at

BT012840.1/Les.4889

2

4.9


BM412424/Les.7840

E2F transcription factor homologue to ATE2FB (AT5G22220 ) Transcription factor homologue to ATDPB (AT5G03415)

-1.4

-2.6


AW032581/Les.8286

Homeodomain transcription factor KNAT4 (AT5G11060)

-3.3

1.7

Les.4929.1.S1_at

BT012922.1/Les.4929

3.4

7.6

Les.4080.1.S1_at

X94947.1/Les.14714

Leucine zipper transcription factor homologue to ATHB13 (AT1G69780) Tomato homeobox protein (VAHOX1) homologue to ATHB1 (AT3G01470)

3.2

-1.4

Tomato transcription factor vsf-1 homologue to basic-leucine zipper family (AT2G21230) bZIP transcription factor homologue to ATBZIP9 (AT5G24800)

2.7

-1.1

-1.9

2.6

Les.4450.1.S1_at Les.198.1.S1_s_at LesAffx.37115.1.S1_at

APETALA1-like MADS-box (LeAP1)

GRAS Les.5190.1.S1_at LesAffx.69645.1.S1_at E2F-DP

Homeobox

bZIP Les.3643.1.S1_at

X73635.1/Les.3643


AI486980/Les.10431

TCP Les.1959.1.A1_at

BG630503/Les.19326

TCP family transcription factor (SlTCP3)

1.7

4.9

BI929558/Les.3065

SBP transcription factor homologue to SPL3 (AT2G33810)

7.5

6.6

BI207626/Les.6253

Plant homeodomain domain containing homologue to AL6 (AT2G02470)

-3.2

-1.4

SBP Les.3065.1.S1_at Alfin-like LesAffx.66562.1.S1_at

Les.1487.1.A1_at

BG626033/Les.1487

Plant homeodomain domain containing homologue to AL4 (AT5G26210)

-2.6

1.2

BT013648.1/Les.1594

Two-component response regulator-like APRR2 (AT4G18020)

3.8

2.3

AI895834/Les.2876

Transcription factor homologue to ATHSFA7A (AT3G51910)

1.2

2.5

-3.1

-1.7

-4.9

-7.7

G2-like Les.1594.1.S1_at HSF Les.2876.2.S1_at Others LesAffx.66054.1.S1_at

AW650464/Les.8014

Sequence-specific DNA binding transcription factor (AT3G58630) LesAffx.44609.1.S1_at BG631285/ Les.13731 Sequence-specific DNA binding transcription factor (AT3G10040) * Fold expression in rin mutant compared to wild type.

Table S5 Identification of CArG boxes on promoters of differentially expressed genes in rin mutant

Sl. No. 1

Name Solyc05g047530.1.1

Chromo some Solyc05

2

Solyc01g067750.1.1

Solyc01

3

Solyc01g067890.1.1

Solyc01

4 5

Solyc01g105660.1.1 Solyc10g081650.1.1

Solyc01 Solyc10

6

Solyc04g080550.1.1

Solyc04

7

Solyc01g009010.1.1

Solyc01

8

Solyc11g071280.1.1

Solyc11

9

Solyc03g007960.1.1

Solyc03

10 11

Solyc10g052490.1.1 Solyc05g052240.1.1

Solyc10 Solyc05

12 13

Solyc10g052510.1.1 Solyc03g117870.1.1

Solyc10 Solyc03

14

Solyc08g081570.1.1

Solyc08

15

Solyc11g013110.1.1

Solyc11

16

Solyc01g097810.1.1

Solyc01

17

Solyc03g031860.1.1

Solyc03

18 19

Solyc10g007600.1.1 Solyc07g042440.1.1

Solyc10 Solyc07

Start (bp) -424 -559 -715 -1537 -192 -748 -1347 -1526 -314 -1067 -1068 -1260 -1454 -1455 -56 -14 -146 -266 -519 -1274 -237 -716 -1347 -123 -266 -915 -517 -936 -1254 -265 -279 -572 -872 -1240 -1437 -883 -1234 -1286 -1128 -10 -866 -50 -360 -1141 -32 -902 -998 -1222 -331 -776 -923 -904 - 944 -1027 -1206 -307 -405 -905 -1224

End (bp) -433 -568 -724 -1546 -201 -757 -1356 -1535 -323 -1076 -1077 -1269 -1463 -1464 -65 -23 -155 -275 -528 -1283 -246 -725 -1356 -132 -275 -924 -526 -945 -1263 -274 -288 -581 -881 -1249 -1446 -892 -1243 -1295 -1137 -19 -875 -59 -369 -1150 -41 -911 -1007 -1231 -340 -785 -932 -913 -953 -1036 -1215 -316 -414 -914 -1233

CArG box in the RIN-binding site sequence (5' to 3') C[TAC][AT](6)[ATG]G TAAAATTTCTccaaataaggTTTTGAAAAA AATGTGGAAActttaaaatgGAATTAGTTC GTCATAATACcaaatatttgTTGATTACAT GGAAAACTCActatttattgTGTGAACAAA CGGTAGTGTCctattatatgGATCTCTTGA AGTGGTTGAGcattaatatgAGTAAGAAAC AGACGTAAAGccatttattgATGTAAAAAT CCAGAATGCAccaaaattggAGATAATATT AGTAGTGTACcttttttaagATTTGAGTTT AGAGTCAAACcattttaaggTACTTTCACT TAGAGTCAAAccattttaagGTACTTTCAC TATGATCAAAccaattttggATACTCTTAC AGGGTCAAGCcattttttggTACTTTACTT TAGGGTCAAGccattttttgGTACTTTACT TTGTTGTCCTcttataaaagTCATCATCAT CCAGGGAGCCcaaaattttgTGAAATAAGA GGGTTTCCAGcaatttaaagAAAAAAAGAT GGAATTTGAAcaatttaaagTGAAAAGATT CAGCAAGCACcaaaaatttgGCCAGCAAAA TTTGGGGAAAcaaaaaaatgAATCTTTTGG TCTTTCACCAcaaatttttgATTTATATAT AGAATTAGTGcatatttttgAAACTCTTAT GACTAATCAAcatttaaaagTCTTCTTCAT TGAAAACTCAccaaaataagAGTAAAGTTT ATTAAAAATCcattaatttgATACAAAAGA GCGGCAACTTcaaaattatgGTCTCATTCT ACAAGTTTGActtatttatgTCATTACCAT AAAAATAAAActtatatatgTGAAAACTAT AGAAACCATCcttattaatgTATGAAAAAA AAATAGTAATcaaaatttagAAGGGAGTGA GATAATTATAcaaaaaatagTAATCAAAAT TTCTATTTTGcctttttaagAAATAAAAGT AAATATTATAcctttttttgAAGGATTGAA CTTGATATTCctttttaaagTAGTTAACCA ATGTTTTTTTcatattaatgAGAAAAATCT AGTAATATCCcaaaaatatgACGGAGAATA ATAACAACAAcaatattttgTTTTTAAAAA AAATGAACATctaaataaagTTCAATATAG CATTTTACTGcaattttttgGGTTAATAAC CCAAATTTTTcctttttttgCTCTCAAAG GTCCTATTCTctattaattgATGAGTAAGT TATCTAATTGcataaatttgAGTTGAAACA TCTTAAATCAcaaaaaaatgTTTTTTTCTT GCCCAAAAGTccaaaattagTAATCAAAAT CGTCACTTTCctataaaaagGAAACAAAAT AAACATTTTAcctttaaatgTAAAATATTT TTGAAGCTCActaaattttgATGTTGCGAT CTAGTATATTcattatttagATCATGATTA AACGTGTCATcaataaatggGAGTGCCTAA TTTTTTTCATcttattttggTATTTGTATG GGCAATTTTAcatttttttgATAAACAATT ATCTTGTTGActaaatatagAATGCATCCA TCTATGTGTAccaaaattagAAAATCAGGC CTTTAAACTTcaaattttggCTCCGCATAC TTTTACCCCTcttaattatgAAGTGAATGA TTATTTACAAcaaatttatgTTATTTCATA TTTCTAATAAcaatatttggTACAAAGACT GTCATGTTTTctttaaaatgAGCCATCAAA ATTTCTCACTctataaatagGATTGTTCAT

Table S5 Identification of CArG boxes on promoters of differentially expressed genes in rin mutant

20

Solyc03g118130.1.1

Solyc03

21

Solyc06g083690.1.1

Solyc06

22

Solyc01g097910.1.1

Solyc01

23

Solyc06g048410.1.1

Solyc06

24

Solyc04g078910.1.1

Solyc04

25

Solyc01g108020.1.1

Solyc01

26

Solyc08g079830.1.1

Solyc08

27

Solyc09g007520.1.1

Solyc09

28

Solyc01g006300.1.1

Solyc01

29

Solyc08g006720.1.1

Solyc08

30

Solyc06g008760.1.1

Solyc06

31

Solyc01g086680.1.1

Solyc01

32

Solyc09g011630.1.1

Solyc09

33

Solyc08g081530.1.1

Solyc08

34

Solyc10g075160.1.1

Solyc10

35

Solyc02g067840.1.1

Solyc02

36 37 38

Solyc09g011590.1.1 Solyc08g062970.1.1 Solyc01g111510.2.1

Solyc09 Solyc08 Solyc01

-1258 -679 -1146 -1169 -1366 -1498 -183 -1374 -223 -877 -1489 -1533 -236 -1344 -79 -918 -1015 -1091 -900 -960 -1015 -1132 -1498 -317 -921 -984 -34 -339 -1129 -568 -986 -1137 -1227 -1371 -189 -948 -1131 -1320 -515 -806 -947 -1215 -98 -302 -465 -1033 -660 -699 -991 -289 -455 -1189 -942 -1140 -686 -687 -1081 -664 -321 -163 -692

-1267 -688 -1155 -1178 -1375 -1507 -192 -1383 -232 -886 -1498 -1542 -245 -1353 -88 -927 -1024 -1100 -909 -969 -1024 -1141 -1507 -326 -930 -993 -43 -348 -1138 -577 -995 -1146 -1236 -1380 -198 -957 -1140 -1329 -524 -815 -956 -1224 -107 -311 -474 -1042 -669 -708 -1000 -298 -464 -1198 -951 -1149 -695 -696 -1090 -673 -330 -172 -701

TATTATGATActtaatatggTGACTTTTGG AAAATAACAAcattttattgATCGACCACT ATTGGTAAATcatttttttgATTAGGTTCC ATTCTAAAAAcaattaaatgTCAATTGGTA TATAACATGTcaaataaaagTAGACGGAGG ATTTGATATGcaaaaaattgTAATTTATAT ATTTTTCTCTccaaattttgAATAAAAAAA TGATCGACCActttaatttgTCCTTTCTCT TTCTAATTTActttttttagTGAGAAAGAA TTTTATGATAcataaatatgTGTACTAACT TAATTTTATTcatatttttgTGCACCTTTT CAGTGACACActttaatttgATAAATATCT ATTATGCAAAcaattttaagAAACTATCAA TTGGTTAACTctaaatatggCTTAAGTCAT GGAATTGTCGctttattatgTGTGGATGTT TATTTATAGGctaaatttagCTCTATCACT GATGAAGTATctaattaaggGAGCATTAAC GAAACACTTActaattatagGAAAAAGGAC TTGTGGTCTCcaatttttagTAGTTTGTTA AAATGGTTGAcattaataagTGATACAACA GTGGATTTAActtttatttgGGGAAATAAC AAAGTGGCTAcaatatatggAGAGAAAAGA CCAGAAGCTAcaaaatatggCGTGTTCAGA AATTTTTTAActatttttagTTTTAAATTA TTAAAATGTActaatttatgTAAAAAAAAT AGATATTTAAcataatattgCTATAAATAA GACATTTCATcaaatattggCCAAAGTACA TATTATCTCCcttttaaaagGCATATTGAC ATCATCCATAcctaaattagTTTTGTTTGT GTAAACAAGTcaaattatagCTTGATTAAA CCTTGCCGCCcataaattagAGCATATATG TGTATGTAGTcaatttaaagAATTTTTACA AAATGTTGGActtatttatgATTGAAGAAA AACACAAAATcgtaatttagTGAAAAAGAA ATAACTTTTGcaattttaagAACTAACTCT CAAATTACACccaaaatttgACTTCATATA ATCATATACActaaaataggGAGAAAGACA TATAGTTTGAccaaaaaaagAAACTATGAC TCAAGAGTGTctaaaatatgTATTCAATCA GAATTAATGActaattatggATAATCATCA AAAAGAATCTcaaaaaattgACAACATATT GTTCAAAATTcattttaatgTTCAAATCC TATTAATATGcaaaaaattgTAATTTATAG TTTAGTCTGAcaaatttttgAATAAAAATA TTATGATCAActtaattttgATTAATTCTC TTATATCATTctttttaaagAGAAGAAATA TTTCATTCGAcattattaggAGGGAAAGTC TCAAAGTAACcaaaatattgATTATGTCTC CAACCTTCATcctttttaagATATTGTCAA CTAGCTTATTcatatattagGCTTGGTGGT TTACCAAGAGcatataaatgTACACAAAAG TTACAATTTCcaaaattaagGATTAGTTTG CTATAAATTAcaattttttgCATATCAATA TAATTATATAcataattatgTTAACATATA GGGCAGACACcttttaaaggAGCAGGCAAC TGGGCAGACAccttttaaagGAGCAGGCAA GAGAAGATGGccatataatgCTGTCTGATT ATTAAAAATTctataaaaagCTCCTTTAAT ATAATTTACActaaatttagAGATACTTTC TATTTACTATccaaatatagATTTCTTTAT GAATTCGAATcttaattttgTAAGAATTTT

Table S6 Primers used in the study

Primer sequences ACO5F: ACO5R: ACS3F: ACS3R: ACS6F: ACS6R: ASC1AF: ASC1AR:

AGAATGGAAACATCAGCAACACA GCTGGACGATGCCAAACAA CCCCGGTTTTCGCATTG CCGCGGAGACAACCATCT CCTGGTGATGCATTTCTAGTTCCT TGTACTCCTGTTCTCCATCTCAAATC GGTGCTCATGAAATGCTTGCT TGGGACCAAAAAGGCATCA

ERF1F: ERF1R: ERF4F: ERF4R: PGF: PGR: PMEU1F: PMEU1R: PECESTF: PECESTR: RTH1F: RTH1R: RTTML: RTTMR:

TGGCTAGGGCACAACAAAGAT GGAGACCCAAGAACCCCAAT CCAATTCCTCATACCCAAATGAA TCGGAGCGGAGATTGAAGTAA GGGCCTTGTAAGTCAGCCAAT TCCATGCCACTGGGTCCTT CGACGGAAGCGGAGATTACA TCTTCTCTGGCGCTTTTCGT TCCTCCTCCTGGACCTA TGGAGCGGGCCTGATTAA TATGTTCTGGTGGCCCG TCTGCTCCTCCGTGAAAG GTTGCTGCTTCAATACCACA CTCCAAAGAGCTTCTAACCTG

RTRBOH1F: RTRBOH1R:

GGAACAGGCAACGGTGTAGACT GCACGCTGCCGACGTAA CGTCGTACAGTGGTCCTTTAAGC CCTCGCGCACTTTTTTCCT TGTGTCCATGGCTCGTATCG GGGTGAGTGTGAGGTGGGTTA AGATTCGTGTTGCCACCATTT TCTTGCCAAGGTCCAATCCT GACTTGGCACCCGTTTTTTC TCGCACCAACTGAATTGTTACAT

RTWFI1F: RTWFI1R: RTOXOF: RTOXOR: RTGLOF: RTGLOR: RTLeGLOF: RTLeGLOR:

Purpose

Quantitative Real Time RT-PCR of fruit ripening related genes in tomato

Quantitative Real Time RT-PCR of ROS producing genes in tomato

Table S6 Primers used in the study

RTSAAP1F: RTSAAP1R: RTSAAP2F: RTSAAP2R: RT-CAT1F: RT-CAT1R: RT-CAT2F: RT-CAT2R:

CATGCGTTTTCTCAGCTGTACG CTCCCATGCGAGTTTCTGC CTTGCGTTTTCTCAGCTGTGAA CTCCCATGCGCGTTTCATT CGCCCATCAAGCGCATAC TGTACACAGGACCACCAGCATT GTTCATGCCCGAGGTGCTA AGGTGAGCAATGTCATGAGTAACTTC

RT-ERCATF: RT-ERCATR: RT-FeSODF: RT-FeSODR: RT-CuZnSOD1F: RT-CuZnSOD1R: RT-CuZnSOD2F: RT-CuZnSOD2R: RT-cevi16F: RT-cevi16R: RT-Lig_perF: RT-Lig_perR: RT-TPX2F: RT-TPX2R: RT-APX6F: RT-APX6R: RT-APX2F: RT-APX2R: RT-APX1F: RT-APX1R: RT-TPX1F: RT-TPX1R: RT-PHG_PerF: RT-PHG_PerR: RT-Glu_perF: RT-Glu_perR: RT-Glu_perPF: RT-Glu_perPR: RT-APXF: RT-APXR: RT-GST/PF: RT-GST/PR: RT-APX_iso7F: RT-APX_iso7R: RT-APX_iso4F: RT-APX_iso4R:

ACCGGAAGCCCACATGTG CCGACTCGGTCTGCCTCTT CCTCACCATCGACGTTTGG CAGGTCGCCGATTCTGAAAG CCGACAAGCAGATTCCTCTCA CATGAACAACAACAGCTCTTCCA GGACGAGCACTTGTGGTTCAT GAGTTCATGGCCACCCTTTC GGAACCTCAGCATGCCAATT GGGCCACCAGTGGAGTTG GGCGTTGTTTCTTGTGCTGAT CCAACCAAGGCAACTCCAA TCCCAAACGCTCCATCTCTT AGCAATCGTGGAAATGCATTC GCCAGAAACAAGATACACGAAAGA CCACTGCACAGTCCATGATTG TCCCATGCTGATTTCCATCA AGGTCCTCCCGTAACTTCAACA CAAAGCGGAGCTAGCACATG GCTCCAAGAGTCTGAGAGCAATG CACTCCCACTTGCAGCATGA TTCAACTCAGCAGCCTTTTCAA GGCAAGAACCCGGAACAA CAGCTTTGAACCTGGTGCATAC GCAAACGAGCAACCCTCAAT CAACGTCCTTGCCCTTAGCA TGCAACCAGTTTGGACATCAG GCCGTTCACTTCAATCTTGTCA TCTCCAGCCTATCAAGGACAAGT CACTGGCCAGCTGGAATAAATC TGTAGAGGCTGAGTGCCCAAA CACTGTCCCTCAGCATACAATTCT GCTTGGGCTGGCACGAT TTGCGGCCACTCCTCAA GAGACCTCCGCGCTCTCA CACGCTAAGCGAAGCATGATC

RTTAL: RTTAR:

TTATCACCATTGGTGCTGAG CGATGTTTCCATACAGATCCTT

Quantitative Real Time RT-PCR of ROS scavenging genes in tomato

Endogeneous control (Actin) for Quantitative Real Time RT-PCR

Table S8: Position of CArG boxes on promoters of selected genes which were not differentially regulated in wild type Vs rin mutant. Sl. No. 1 2

Name

Chromosome

Solyc04g078540.2.1 Solyc07g062970.2.1

Solyc04 Solyc07

3

Solyc01g093960.2.1

Solyc01

4

Solyc10g074500.1.1

Solyc10

5

Solyc05g054700.2.1

Solyc05

6

Solyc11g067280.1.1

Solyc11

7

Solyc02g087670.2.1

Solyc02

8

Solyc05g013880.1.1

Solyc05

9 10

Solyc08g081020.1.1 Solyc06g008290.2.1

Solyc08 Solyc06

11

Solyc06g034390.1.1

Solyc06

12 13

Solyc07g064620.1.1 Solyc05g053140.2.1

Solyc07 Solyc05

14 15 16 17

Solyc11g005080.1.1 Solyc12g006160.1.1 Solyc06g018050.2.1 Solyc08g008070.1.1

Solyc11 Solyc12 Solyc06 Solyc08

18

Solyc04g080190.2.1

Solyc04

19

Solyc03g120500.2.1

Solyc03

20

Solyc01g108890.2.1

Solyc01

21

Solyc08g065610.2.1

Solyc08

22 23 24 25 26 27

Solyc12g056090.1.1 Solyc02g062020.2.1 Solyc08g061320.2.1 Solyc04g082660.2.1 Solyc02g067320.1.1 Solyc12g042430.1.1

Solyc12 Solyc02 Solyc08 Solyc04 Solyc02 Solyc12

28

Solyc11g056450.1.1

Solyc11

29 30

Solyc01g105330.2.1 Solyc08g076540.2.1

Solyc01 Solyc08

31

Solyc07g056550.2.1

Solyc07

Start (bp) -100 -363 -1278 -1279 -222 -545 -745 -349 -1072 -366 -714 -602 -1157 -1333 -121 -315 -686 -725 -924 -45 -903 -56 -180 -694 -1160 -1207 -461 -661 -255 -407 -631 -1384 -1460 -226 -388 -898 -1128 -767 -1330 -898 -1355 -994 -625 ***** ***** ***** -925 -1169 -1316 -798 -987 ***** -413 -1396 -404 -616

End (bp) -109 -372 -1287 -1288 -231 -554 -754 -358 -1081 -375 -723 -611 -1166 -1342 -130 -324 -695 -734 -933 -54 -912 -65 -189 -703 -1169 -1216 -470 -670 -264 -416 -640 -1393 -1469 -235 -397 -907 -1137 -776 -1339 -907 -1364 -1003 -634 ***** ***** ***** -934 -1178 -1325 -807 -996 ***** -422 -1405 -413 -625

CArG box in the RIN-binding site sequence (5' to 3') C[TAC][AT](6)[ATG]G TAATTTCAATcttaaaaaagAAAGATAATT AAAATTCCAGccaaatttagATAAATATAT AAAATTAATCcaattttaggGACCACCAAATAA AATTAATccaattttagGGACCACCAA AAAATTAACCcaaaataaagCGCGGCCAAA GCACTTAATTcatttttaagTGAATTTAAA ATAGCTTGTTctatttattgCCTAGTGATA TATGATCCATccttttttagCTTTGGAAAA TCTAAAAGGAccatttaaagAAGCTATAGT AATAATCAACcttattaatgAGTCTCTTTT TTAAAAACACccaatttatgCTATGTATTG ATTTTTTGTGcaaatttaggAACTTTCAAG GTTAACTCATcatttattagAAGTGACCTA GTCAGCAAAAcaaataaaagAGCAGTACTT TACGTTGCTGcttttttaggCTACAACAAA TATCAACCAActaattaatgTCTTTAGAGG ATAACTAAACcataaatatgTGTCTCGATT TTAAAACGTAccattaaatgCTTAAGGAAT AATTAAGGTAcatattttggGCAAACAAAG TAAATTTTAActattattagTTGACTCAAT CCATTTATTTcaaaatattgAGAAGAAACT TTGGACATGTcaataatttgTTGTTTATTA ATTTATTTTTctttattatgTGTTATTAGG CACGTGTTTTctttaaaatgTAGTTGGAGA TTATTAAACAcaatttattgTCAGAAATTG AAGCAAAAATccatatttagCAAAAAACTA TCTAATTGTGcaataaaaagTGATTAATGT AATCAAAATTctaaattatgTTTTCATGCA ATTTATATTTctaaaaatagCATTATGATA AAAGATATTActattttaagTTCTAACTCA GGTTGAGCCGcttatttaggAGGACACTTT CTAACAAGACctaaattatgGGGTTGTTGA CAAAAGGTGGcatttttatgAGGAAAAAAA CATATAAGATctttaaattgTTTATAAAAA TTTCAAAATTcattattttgGCCTAGAAGA AAAAATTAAActattttttgTCTATATAAT ATATACCCTTcatttaatggGAGTTAAAAA AGACTTTCAGccttattttgAATGAAGATA TTTGGTCTCAcaaaaattagGTTACCACTG AATATTTCGTcatttttttgAAGTATCACA AAATTAACTCctataaaatgGAATAGTCCT GATAAATTTTcattaaaatgTGTAATGTCG AGCAAGTTGCcatttttaagCCTTTTGATG ************ ************ ************ TACTACATAGcaaatatatgATAAGTTTTC TCCCCATACAcattaataggCAGTTTCTGC GAAGTGTAGAcaattttttgCTGATTCCCC CCCGCTCCCAcaaaaaaatgTTTCCTAGGC TCATTTAAGGccttttaaggACTTGTGAGG ************ ATACCTTTGActtattttagATTAAATTTT ATCTCTTTCCctttttttagTTAGTTTAAA CTTGCTTTAAcaaaaaaatgATTATTAACA GTATCATTTActaaaattagAGCTAGAAAC

32 33 34 35 36

Solyc02g071170.2.1 Solyc01g090600.2.1 Solyc04g076870.2.1 Solyc08g066680.2.1 Solyc05g021390.2.1

Solyc02 Solyc01 Solyc04 Solyc08 Solyc05

37

Solyc09g009190.2.1

Solyc09

38

Solyc05g025890.1.1

Solyc05

39

Solyc08g080900.2.1

Solyc08

40

Solyc02g071330.2.1

Solyc02

-715 -912 ***** -882 -1453 -1277 -355 -489 -1338 -683 -979 -1006 -1053 -1128 -1242 -477 -651 -811 -1242 -719 -1382 -220

-724 -921 ***** -891 -1462 -1286 -364 -498 -1347 -692 -988 -1015 -1062 -1137 -1251 -486 -660 -820 -1251 -728 -1391 -229

AAGTAACATActataatatgCCTAACTTTG CTCAGTTTAActttaaaatgTATGATTTAA ************ TACTCAGATAcattaatatgTAGCTTTCAT AAACCCTAACcctaaatttgTATTGTTGGA ATATGCATACcttattttagTCAAAAATAA GGTTTTACCActttaaaaggTCACTTTGTT AATATATAAAcaattaaatgCAAGAAGTTT CTAATGAATAccatttattgAATCTAACCT TGTATATAATcttttaattgGAGTAATACT TAGAAAGGCCctttaaaaagTTTTTTTTAT TACTATATTActtaattatgATGAAATTAG ATATTTATCActaataattgTGGTTAATTA GAAGTTTCCAcaaaatatggACTCTATAAA AGAACTCCACctttttaatgGAAAAAAATA GTTAAGTTGTctatttattgGCATATATTT TTAGTGGATAcaattattagGTAAAGGTAT CAAAAAATTCcatttaaaagGAAAAATATT TCTTACTTCTcatattaaggTAAAACTTAT AAATTGCACCctttaatatgCTCGTGGATA ACCGCTACTGctaaatttggTTAGCTGAGG ATACAACTAActaattaatgGAAAATATCT

Fig S1 Functional categorization of differentially

Fig S1 Functional categorization of differentially

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