Supplementary data Transcription factors, sucrose ... - Semantic Scholar

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peonidin 3-(coumaroyl)-glucoside. 609. 301,463. 8.2. MR malvidin 3-rutinoside. 639. 331, 493. 8.8. DCRG delphinidin-3-(coumaroyl) rutinoside-5-glucoside.
Supplementary data

Transcription factors, sucrose and sucrose metabolic genes interact to regulate potato phenylpropanoid metabolism

Raja S Payyavula, Rajesh Singh, and Duroy A Navarre*

A

Supplementary Fig. S1.

Payyavula et al., 2013

B

Supplementary Fig. S1 continued.

2

Payyavula et al., 2013

3

C

D

Supplementary Fig. S1 continued. Protein sequence alignment of representative (A) MYBs, (B) bHLH, (C) WD40 and (D) AOMT from potato and from other species. Accession numbers are listed in Fig. 2 or Supplementary Table 3.

Payyavula et al., 2013

a

b

2

White Yellow D.yellow Red Purple

60 a b

40

c

1

d

20

µmol TE g-1

nmoles CA min-1 mg -1 protein

3

4

e c d d

0

0 PAL activity

FRAP

Supplementary Fig. S2. PAL enzyme activity and FRAP antioxidant activity in the five genotypes. The data represents the means ± SE of three biological replicates. Values with same letter are not significantly different (p< 0.05).

Payyavula et al., 2013

5

A

B

Supplementary Fig. S3. (A) StAN1 protein sequence of the five potato genotypes used in this study. Differences are shaded in black. Coding regions were sequenced and translated. (B) StAN1 promoter region from four genotypes used in this study. 1500 bp were sequenced and a 700 bp region containing the SURE and jasmonate motifs starting 500 bp upstream of the start codon were aligned as shown. Methyl jasmonate responsive motifs are highlighted in red. Sugar responsive elements (SURE) are highlighted in green.

Payyavula et al., 2013

Relative expression

0.08

a

a

ab

2.4

a

ab

0.06

cd

ab

0.04

bc

1.6

b

bc bc

6

Wiseman Fairbanks Palmer Juneau Texas Florida

0.8

c

0.02 d cc

0

0 bHLH1

WD40

AN1

Supplementary Fig. S4. Expression of selected transcription factors in purple potatoes grown in in Alaska (Wiseman, Fairbanks, Palmer and Juneau), Texas and Florida. AN1 expression uses the y-axis on the right. The data represents the means ± SE of three biological replicates.

Payyavula et al., 2013

72h

48h AB

7

A

AB

A

Supplementary Fig. S5. Tobacco leaves 48h and 72h after infiltrating with a binary construct harboring AN1 (A) alone or AN1 + bHLH1 (AB).

Payyavula et al., 2013

8

mAU 300

A

AN1

1.0

287.1

E

m/z 595

M/Z 595

449 0 300

AN1

B

m/z 611

0.0 1.0

F

303.1

M/Z 611

465.1 0 AOMT3

300

C

0 300

m/z 625

AOMT3+AN1 m/z 611

D

0.0 1.0

0.0 1.0

449 316.8

G

M/Z 625

478.8

273.8 330.8

H

M/Z 639

m/z 639 286.7

0

492.7

0.0 1

2

3

4

5

6

7

8

9 min

200

300

400

500

600 m/z

Supplementary Fig. S6. MS extracted ion data of the most abundant anthocyanins formed in (A) N. tabacum (Samsun) infiltrated with AN1; (B) N. benthamiana leaves infiltrated with AN1, (C) AOMT3 and (D) AN1+AOMT3. MS2 data for the indicated peaks is shown in panels E-H.

nmoles CA min-1 mg -1 protein

Payyavula et al., 2013

9

6 5 4 3

E B W A

2 1 0 PAL activity

Supplementary Fig. S7. PAL activity in tobacco leaves infiltrated with empty vector (E), bHLH1 (B), WD40 (W) or AN1 (A). The data represents the mean ± SE of three biological replicates.

Payyavula et al., 2013

10

Phn

Phenolics

1

Anthocy 0.95

Anth

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

Asc

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

Phe

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

3CGA

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

C4CGA

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

5CGA

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

4CGA

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

-0.1

1

Rut

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

Kmp

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

-0.12

1

BDCS

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

0.21

1

BCSD

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

PALe

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

FRAP

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

CHS

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

DFR

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

UFGT

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

AOM12

  

  

  

  

  

  

  

  

  

  

  

  

  

  

  

1

AOM3

  

  

  

  

  

  

  

  

  

  

  

  

  

  

0.03

1

PAL

  

  

  

  

  

  

  

  

  

  

  

  

  

1

HQT

  

  

  

  

  

  

  

  

  

  

  

  

1

HCT

  

  

  

  

  

  

  

  

  

  

  

1

C3H

  

  

  

  

  

  

  

  

  

  

1

AN1

  

  

  

  

  

  

  

  

  

1

AN2

  

  

  

  

  

  

  

  

1

M73A

  

  

  

  

  

  

  

1

M73B

  

  

  

  

  

  

0.47

1

M75B

  

  

  

  

  

1

M75C

  

  

  

Ascorbate -0.93 -0.87

Phe -0.65 -0.63 0.37

3CGA -0.07 -0.24 0.09 0.33

C4CGA -0.16 -0.33 0.13 0.44 0.99

5CGA 0.97 0.89 -0.93 -0.67 -0.19 -0.25 4CGA 0.01 -0.18 0.01 0.3

1

0.98

Rut 0.64 0.81 -0.52 -0.37 -0.09 -0.19 0.47 -0.07 Kmp 0.65 0.48 -0.71 -0.5 -0.28 -0.28 BDCS 0.49 0.38 -0.15 -0.81 0.25

0.14

0.81

-0.2

0.43

0.27 0.28

BDCSD -0.19 -0.36 0.3 0.17 0.94 0.92 -0.28 0.92 -0.2 -0.32 0.43 1 Glu    Glucose 0.87 0.89 -0.97 -0.27 -0.19 -0.23 0.85 -0.11 0.64 0.55 0 -0.43 1 Suc Sucrose 0.92 0.89 -0.89 -0.69 -0.42 -0.47 PALe 0.97 0.88 -0.93 -0.66 -0.16 -0.22 FRAP

1

0.97 -0.92 -0.67 -0.12

-0.2

0.97 -0.33 0.46 1

0.81 0.33 -0.49 0.83

-0.07 0.45 0.82

0.97 -0.04 0.67 0.63

1

0.43 -0.26 0.84 0.96

0.49 -0.23 0.87 0.92 0.96

CHS 0.97 0.93 -0.93 -0.67 -0.28 -0.36

0.99

-0.21 0.54 0.77

0.36

DFR 0.8

-0.32

0.92

-0.21

0.28 -0.36 0.69 0.91 0.92 0.78 0.89

UFGT 0.97 0.94 -0.93 -0.66 -0.28 -0.35

0.99

-0.2

-0.02

0.66 -0.82 -0.59 -0.3

AOMT1-2 -0.2 -0.45 0.22 -0.15 0.13

0.17

AOMT3 0.92 0.85 -0.91 -0.65 -0.31 -0.36

0.1

0.98

0.55 0.76

-0.4 0.88 0.98 0.98 0.96

0.37 -0.39 0.88 0.98 0.98 0.97 0.99 0.88

0.14 -0.83 0.48

0.23

0.3

0.99 -0.22 0.37 0.87

0.34

-0.4 0.83 0.99 0.98 0.92 0.98 0.96 0.98

-0.4 -0.1

0

0.39 -0.38 0.87 0.99 0.99 0.97

PAL 0.97 0.93 -0.93 -0.68 -0.28 -0.35

0.99

HQT 0.07 -0.1 -0.08 0.32 0.98

0.97

-0.05 0.99 0.02 -0.19 0.23 0.87

HCT 0.44 0.17 -0.5 -0.32 0.06

0.08

0.6

0.14 -0.41 0.91 0.25 0.05 0.28 0.53 0.62

C3H 0.65 0.42 -0.56 -0.69 0.02

-0.02

0.76

0.09 -0.11 0.88

AN1 0.9

0.81 -0.88 -0.67 -0.31 -0.36

AN2 -0.24 -0.33 0.55 -0.49 0.09

0.54 0.77

0.98 -0.23 0.31

0.9

-0

1

0.89

-0.3 -0.02 0.02 -0.2 -0.2

1

-0.11 0.98

-0.14

0.04

-0.17 -0.1

0.5 0.82 0.49

0.73

0.64

0.62 0.08 0.34 0.69 0.78 0.62 0.67 0.86 0.67

0.61

0.76 0.69 0.06 0.89

0.36 -0.39 0.79 0.98 0.98 0.89 0.97 0.98 0.96

0.11

0.4

1

0.51 0.1

0.97 -0.2 0.69 0.81

-0.22 0.05 -0.31 -0.09 0.69 0.42 -0.7 -0.2 -0.22 -0.24 -0.3 -0.2 -0.28

0.56

-0.24 -0.3

MYB73A -0.56 -0.49 0.39 0.31 -0.67 -0.56

-0.4

0.25

-0.24 -0.4 -0.7

MYB73B 0.04 -0.1

0.25 -0.43 -0.56 0.69

0.8

0.36 0.22 -0.5 0.69 0.67 0.43

0

MYB75B -0.02 0.06 0.03

0.04

-0.2

-0.24 -0.1 0.28 -0.15

-0.48 -0.46 -0.44 0.4

0.68

0.64

-0.69 -0.59 0.04 -0.68 -0.61 -0.3 -0.2 -0.41 -0.55 -0.3 -0.1 -0.35

-0.24 0.65

0.5

-0.66

0.21 -0.28 -0.2 0.33 0.26 0.03 0.21 0.56 0

0.2

-0.1 0.07 0.28 -0.18 -0

-0.27 -0.21 -0.08 0.47

0.53 0.07 -0.4 -0.23 -0.02 -0.2 -0.6 -0.22 -0.63 -0.37 -0.2 0.71 -0.6 -0.51 -0.43 -0.28

-0.66 -0.95

MYB75C -0.41 -0.4 0.67 -0.42 -0.27

-0.3

-0.35 -0.32 -0.35 -0.16 0.42 0.06 -0.7 -0.3 -0.37 -0.39 -0.4 -0.2 -0.37

0.45

-0.32 -0.4 -0.4

0.54 -0.47

1

M12B

  

  

  

MYB12B -0.73 -0.81 0.65 0.75 0.73

0.79

-0.78 0.67 -0.51 -0.61 -0.26 0.73 -0.7 -0.9 -0.76 -0.76 -0.9 -0.7 -0.84

0.2

-0.82 -0.8 0.63 -0.2 -0.45 -0.81 0.12

-0.03 -0.36 0.48

0

1

bHL1

  

  

0.98

-0.2 0.48 0.66 0.96 -0.28

-0.35

0.19 -0.22 -0.36 -0.85

1

bHL2

  

0.55 0.42 -0.6 0.65 0.45 0.57 -0.28

0.63

0.71 -0.83 -0.1 -0.5

0.4

1

W40

bHLH1 0.97 0.94 -0.93 -0.67 -0.28 -0.36

0.99

bHLH2 0.2

0.42 -0.56 -0.38 0.79 -0.35 -0.67 0.34 0.53 0.41 0.19 0.42 0.71 0.41

0.13 -0.4 -0.12 -0.62 -0.55

WD40 0.94 0.86 -0.91 -0.68 -0.25

-0.3

1

-0.21 0.56 0.75

-0.16 0.4

0.86

0.37

0.4

-0.4 0.89 0.99 0.98 0.97

1

0.88

1

-0.33 0.82 0.98 0.99 0.94 0.98 0.95 0.98

-0.16 0.4 0.04

1

1

-0.1 0.07 -0.26

0.99 -0.1 0.65 0.79 0.99

0.91

-0.2

0.28

-0.32 0.33 -0.33 -0.31 -0.8 0.98 0.49

magnitude of change 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.89 >0.99 greater than zero less than zero

Supplementary Fig. S8. Correlation analysis of transcript and metabolite expression in tubers from five potato genotypes. Pearson correlation coefficients are shown.

1

Payyavula et al., 2013

11

Supplementary Table S1. Retention times and MS data of select compounds present in potato extracts separated by HPLC. RT

Abbreviation Compound

m/z

MS/MS (m/z )

1.8

Asc

ascorbic acid

175 (M-H)

115, 87, 71

2.5

Tyr

tyrosine

180 (M-H)

163, 119, 93

4.0

Phe

phenylalanine

164 (M-H)

147, 148, 72

5.9

Trp

tryptophan

203 (M-H)

159, 116, 142, 186

6.5

3CGA

3-o -chlorogenic acid

353 (M-H)

191, 179, 135

7.0

CP

caffeoyl putrescine

251 (M+H)

234, 163, 89, 115

7.6

C4CGA

cis-4-chlorogenic acid

353 (M-H)

173, 179, 135, 191

8.3

5CGA

5-o -chlorogenic acid

353 (M-H)

191,179, 161,135

8.4

BDCS

bis-dihydrocaffeoyl spermine

531 (M+H)

293, 222, 513, 165, 367

8.5

4CGA

4-o -chlorogenic acid

353 (M-H)

173, 179, 191, 135

9.1

C5CGA

cis-5-chlorogenic acid

353 (M-H)

191, 179, 173

9.6

BDCSD

bis-dihydrocaffeoyl spermidine

474 (M+H)

222, 457, 165, 310, 236

10.4

FQA1

feruloyl quinic acid1

367 (M-H)

161, 135, 335

11.5

FQA2

feruloyl quinic acid2

367 (M-H)

179, 135, 191, 161, 143

12.0

TDCS

tris-dihydrocaffeoyl spermine

695 (M+H)

293, 222, 531, 474, 457

12.3

QRG

quercetin rutinoside-glucoside

771 (M-H)

591,300, 301, 609

12.6

QDG

quercetin diglucoside

625 (M-H)

300, 301, 445 607, 463

12.8

Myr

myricetin rutinoside

625 (M-H)

317, 316, 287, 607,461, 271

13.4

KRG

kaempferol rutinoside-glucoside

755 (M-H)

575, 285, 593

13.5

TDCSD

tris-dihydrocaffeoyl spermidine

638 (M+H)

456, 474, 293, 222

14.0

Rut

quercetin 3-rutinoside

609 (M-H)

301, 609, 271, 343

14.6

Kmp

kaempferol 3-rutinoside

593 (M-H)

285, 593, 431

14.8

RR

rhamnetin rutinoside

623 (M-H)

315, 300, 316, 271

15.4

Glyc

solanine

852 (M+H)

706, 398, 560

15.4

Glyc

chaconine

868 (M+H)

398, 706, 722, 560, 380

Payyavula et al., 2013

12

Supplementary Table S2. Retention times and MS data of anthocyanins in potato phenolic extracts separated by HPLC. RT

Abbreviation Com pound

[M] + m /z

MS/MS (m /z)

3.5

PtRG

petunidin 3-rutinoside-5-glucoside

787

625,317,479

3.8

PlRG

pelargonidin 3-rutinoside-5-glucoside

741

579,271,433

3.9

DR

delphinidin 3-rutinoside

611

303, 465, 449

4.6

DRG

delphinidin 3-rutinoside-glucoside

773

303,611,465

5

CR

cynanidin 3-rutinoside

595

287,449

5.2

MRG

malvidin 3-rutinoside-5-glucoside

801

639,331,493

5.4

PlG

pelargonidin 3-glucoside

433

271

6.1

PlDGG

pelargonidin 3-diglucoside-5-glucoside

757

271,595

6.2

PeR

pelargonidin 3-rutinoside

579

271,433

6.3

PtR

petunidin 3-rutinoside

625

317,479

6.5

PlR

pelargonidin 3-rutinoside

579

271,433

7.4

PoCG

peonidin 3-(coumaroyl)-glucoside

609

301,463

8.2

MR

malvidin 3-rutinoside

639

331, 493

8.8

DCRG

delphinidin-3-(coumaroyl) rutinoside-5-glucoside

919

303,757,465

8.9

PlCRG

pelargonidin 3-(coumaryol) rutinoside-5-glucoside

887

725,271,433

9.06 PtCfRG

petunidin 3-(caffeoyl) rutinoside-5-glucoside

949

787,317,479

9.3

PlCRG

pelargonidin 3-(coumaroyl) rutinoside-5-glucoside

887

725,271,433

9.7

PeCRG

peonidin 3-(coumaroyl) rutinoside-5-glucoside

917

301,755,463

9.8

PlCDG

pelargonidin 3-(coumaroyl) diglucoside-5-glucoside

903

741,271,433

10.1 CCRG

cyanidin 3-(coumaroyl) rutinoside-5-glucoside

903

741,287,449

10.3 PtCRG

petunidin 3-(coumaroyl) rutinoside-5-glucoside

933

317,771,479

11

pelargonidin 3-(coumaroyl) rutinoside-5-glucoside

887

725,271,433

11.1 PtFRG

petunidin 3-(feruloyl) rutinoside-5-glucoside

963

317,801,479

11.4 PeCRG

peonidin 3-(coumaroyl) rutinoside-5-glucoside

917

755,301,463

11.8 MCRG

malvidin 3-(coumaroyl) rutinoside-5-glucoside

947

785,331,493

12

pelargonidin 3-(feruloyl) rutinoside-5-glucoside

917

755,271,433

12.3 PtCR

petunidin 3-(coumaroyl)-rutinoside

771

317,479,245

12.5 MFRG

malvidin 3-(feruloyl) rutinoside-5-glucoside

977

331,815,493

13.3 PlRG

pelargonidin rutinoside-5-glucoside

725

271,433

13.7 PeRG

peonidin rutinoside-5-glucoside

755

301,463

PlCRG

PlFRG

Payyavula et al., 2013 Supplementary Table S3. List of primers used in this study. Species Primer

Potato

Vector

StMYB73A-F StMYB73A-R StMYB73B-F StMYB73B-R StMYB12A-F StMYB12A-R StMYB12B-F StMYB12B-R StAN1-F StAN1-R StAN2-F StAN2-R StMYB75A-F StMYB75A-R StMYB75B-F StMYB75B-R StMYB75C-F StMYB75C-R StMTF1-F StMTF1-R StMTF2-F StMTF2-R StMYB10-F StMYB10-R StWD40-F StWD40-R StbHLH1-F2 StbHLH1-R2 StbHLH2-F2 StbHLH2-R2 StAOMT-1/2F StAOMT-1/2R StAOMT-3F StAOMT-3R StAN1-F-FL StAN1-R-FL StbHLH1-F-FL StbHLH1-R-FL StWD40-F-FL StWD40-R-FL 35S-F pORE-F pORE-R

Primer sequence GCCAGACAAGGTATTTGTGCCGTT TGCGATTAGCAGCTCTATCCCTGA GCCGGTGGTTGATAAACCGATTCC GCATTCCTTATTGCATCRGTCTGC TGTTTATGGGACGGAGAAGGAG GCCAAGTTACCAAATCACTCTGCATGG AGGAGATTATGCCAGACGTGGTGA CATGGTGGCGTTGGCCATACTAAT AAGTATGGGCAAGCCAATGCCA GCCCACCATTGCATATCGTTGTTGTC AGACCTCAACCTCGGAACTTCTCA GTCCACCATTGAACTCCATCGTCT CACTCCTCAAGTTGTGTTTGTCCC TGAAGCTATGTTGCTCGGGCTCTT TGCACCAAAGCCCATAAGGATTTC GCAGCTTTCTCCCATAAGAATTTCA TGGTCCCTCATTGCCGGAAGAATA GCGGCTCATTTCCTTGTCCTTTGA AGCAAACTCCAGATGCATTGATGG CCTTGTTGCATGGAGTTACCTTCACC TGCTGAAAGCAAAGGTGGAATGGG TAATAGCCTCAGTTTCAGCCTCAGGG GCATCAAGATTGCCAGGAAGAACAG AGTGGATGGTAGATCATTGTGTTGT ATTCAAGTCAAGAATCGCATCTCCG GAACTCTTCGATAAAGCTYCCGAC TCTCTTGGAYGGTGTAGTGGAACT AACAGCGGATGACGGAGTATTGCT AGGCSAGATCAGCAAGACGATCAA AGCTCTCGCTCCAAAGACAACTCA CCTGTTCTTGACAAACTCCTGGAAG TCAYCAGCTKCATTAGTCTCTCGT GGTGAAAGTTGGAGGAGTACTTGGCT TGCCTTTAATCCTGGTGGCATAGG AATGCGGCCGCATGAGTACTCCTATGATGTGTAC CCGGGTACCTTAATTAAGTAGATTCCATATATC AATGCGGCCGCATGGAGATTATACAGCCTAATAGC CCGGGTACCTTAATTAGCTCTAGGGATTATCTG AATGCGGCCGCATGGARAATTCAAGTCAAGAATCG CCGGGTACCTTATACTTTAAGCAGCTGCAACTTG CAAGACCCTTCCTCTATAT ACTGAAGGCGGGAAACGACAATCT AGCGGATAACAATTTCACACAGG

Used for

Accession no or Potato Genome Contig PGSC0003DMS000002386 PGSC0003DMS000003180 PGSC0003DMS000001330 PGSC0003DMS000000077 PGSC0003DMS000000121 PGSC0003DMS000000777 PGSC0003DMS000000511 PGSC0003DMT400031607

QPCR

PGSC0003DMT400085829 EU310399 PGSC0003DMS000000013 PGSC0003DMT400060168 PGSC0003DMT400001513 PGSC0003DMT400033569 PGSC0003DMT400032139 PGSC0003DMT400006134 and PGSC0003DMT400006136 PGSC0003DMT400016512

Cloning

13

Payyavula et al., 2013 Supplementary Table S3 continued. Species Primer

Primer sequence

NtINV1-F    TTAGAGACCCAACGACTGCTTGGA NtINV1-R    ACCCGTTTGCCTCATCGGTTGATA NtSUSY-F TTCACCTCAYGGATATTTCGCCCA NtSUSY-R AGTCCTTGCTCCTTTATGCGCT NtCHS-F ACTTGGYAAAGAGGCWGCCCAA NtCHS-R CGGCAAAGCAACCTTGTTGGTA NtPAL1/4-F TTCGCCTACGCTGATGATCCTT NtPAL1/4-R TGCAGCTCTTGCACTCTCAACT NtPAL2/3-F ACCCACTGATGCAGAAACTAAGGC NtPAL2/3-R GCAATTGCAGGGTTCCCAYTTT NtDFR-F ATTCATCTGCGCRTCCCATCAT NtDFR-R AAATACACCACRGGCAAGTCCT Tobacco NtF3H-F AGGCYTTAACCAAGGCATGTGT NtF3H-R CGGGCTGAACAGTRATCCAAGT NtBHLH1-F ATGKGCGCAAACGAGGTTGATAGC NtBHLH1-R TRGCTGAGGTTGTTGTTGCTCA NtINV1-F    TTAGAGACCCAACGACTGCTTGGA NtINV1-R    ACCCGTTTGCCTCATCGGTTGATA NtINV2-F    TATACCGGGTCAACCAACGAGTCA NtINV2-R    CATTTGCCTTGTGGTGTGGTCCAT NtActin-F            AAGCTGTGTTGTCCCTATACGCCA NtActin-R            ATCGCGGACAATTTCCCGTTCA NtELF-F                TGAACCATCCAKGACAGATTGG NtELF-R                TGGGCTCCTTCTCAATCTCCTT

Used for

Accession no AJ305044 AB055497 AF311783 M84466/EU883669 D17467/X78269 AB289448

QPCR

AB289450 HQ589208/HQ589209 AJ305044 HM022269 AB158612 D63396

14

Payyavula et al., 2013

15

Supplementary Table 4. Protein similarity matrix of transcription factors from different species. (A) MYB (B) bHLH and (W) WD40. Accession numbers are listed in Fig. 2.

Payyavula et al., 2013

16

Supplementary Table S5. List of regulatory elements in promoters of different genes from S. tuberosum group Phureja. The numbers in each column represent the position of the element in the promoter sequence relative to the ATG start codon. Promoter elements (sequence) Genes

MYBCORE (CNGTTR)

MYBPLANT (MACCWAMC)

MYCCONSENSUS (CANNTG)

SURE (AATAGAAAA)

AN1

-1380, -1279, -786

none

-1349, -13

-604, -561, -521

bHLH1

-737, -703

-949

-1466, -1154, -960, -510, -409

none

WD40

-1422, -1132, -1096, -908, -678, -437, -133 -63

-1150, -1123, -956, -711

-214

PAL1

-825, -271, -268

-1404, -337

-1385, -1346, -189

none

HQT

-1021, -569

none

-1299

-1082

C3H

-1368, -1329, -1217, -1079, -1067, -576

none

-1271, -1238, -1211, -1067, -1040, -614, -576, -526

none

HCT

-92

none

-872, -656, -597

-178

CHS

-366

none

-1336, -1171, -200, -178

none

F3H

-1082

none

-477, -335, -137

none

DFR

-1395, -1207, -1106, -1039, -874

-189

-1236, -1135, -884, -813, -561, -403, -331, -160, -46 none

ANS

-1330, -1203, -747, -628, -625

-386, -171

-747, -617, -521, -344, -227

none

SUSY1

-1396, -1365, -573, -541, -445, -51

-1299, -1086, -645

-1257, -1067, -998, -846, -730, -685, -7

-1279, -666

SUSY4

-1012, -271, -240, -202

-848

-1289, -1132, -650, -444, -240, -214, -202

none

INV1

 none

-1442, -203

-1396, -1373, -1339, -1142, -1130, -1079, -1049

none

INV2

-717, -548, -83

-539, -476, -259, -198

-980, -622, -124, -83

none