Supplemental Material to

Landes Bioscience

www.landesbioscience.com

Supplemental Material to: Frank Jühling, Joern Pütz, Catherine Florentz and Peter F. Stadler Armless mitochondrial tRNAs in enoplea (nematoda) 2012; 9(9) http://dx.doi.org/10.4161/rna.21630 http://www.landesbioscience.com/journals/rnabiology/article/21630

Supplementary Material Suppl. Table 1: The mitochondrial genomes of Chromadorea analyzed within this study. All genomes are listed in the curated RefSeq database. Taxonomy Organism Chromadorea Ascaridida Anisakis simplex Ascaris suum Toxocara canis Toxocara cati Toxocara malaysiensis Oxyuroidea Enterobius vermicularis Rhabditida Ancylostoma caninum Ancylostoma duodenale Angiostrongylus cantonensis Angiostrongylus costaricensis Bunostomum phlebotomum Caenorhabditis briggsae Caenorhabditis elegans Cooperia oncophora Haemonchus contortus Heterorhabditis bacteriophora Necator americanus Steinernema carpocapsae Strongyloides stercoralis Spirurida Brugia malayi Dirofilaria immitis Onchocerca volvulus Tylenchida Radopholus similis

1

Accession NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC NC

007934 001327 010690 010773 010527 011300 012309 003415 013065 013067 012308 009885 001328 004806 010383 008534 003416 005941 005143 004298 005305 001861 013253

Suppl. Figure 1: The full set of detected mt-tRNAs in 9 Enoplea species. The NCBI taxonomy was used for sorting the sequences which were aligned with Infernal. The conservation scores plotted below the alignments were calculated using ClustalX, normalized and squared to improve the readability.

Dorylaimidia Mermithida

tRNAAla Trichocephalida


tRNAArg Trichocephalida


tRNAAsn Trichocephalida


tRNAAsp Trichocephalida


tRNACys Trichocephalida


tRNAGln Trichocephalida

NC_005928 G

GAGAT t G t aGCT T - - g c t AAGT aT CGCT t t t g c a t AGCGA - a g g t t . . T t AT CT C g

Y

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

CGGGA g T a a CGGAAT T a a GAAT T T t t a AAAGA t t t a AAAGAG t t a CGGGAA c t t GAAT T t T t a -

S1 S2 S1 Y Y nad5 cox1

nad1 cob L1 N N N cox3

-

-

-

t t t -

- - . . . - - aa t tat - - - tc

. . . t

. . -

. . -

. . -

. . -

g t T T CA t aAT T T A t aAT T AA t a c T CAT t t AT CAT t t T AAAA t t AT CAT t

t t t t t t t

t t t t t t t

g c a aT GAA t . g c a aT AAAT t g c a aT T AAT t g c a aAT GA t t g c a aAT GAT t g c a t TTTTA t g c a aAT GAT t

aa . t aa . t aa . t a.gt . . . t aaa t a. . .

t a aA aT CT CG t a a aAAT T T CG t a a a t GAAT T C g . . . t t T CT T T a t . . t T T CT T T a a c a aT T CT CG t . . . A t AAT T C t

NC_002681 L1 GGGT T Ga t aAT GT a t t c aGCAT aT CT T T t t t g c a aGAAGA - a a g t t a . c CAAT CC a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . ) ) ) ) ) ) ) . Conservation:

C

NC_005928 cox1

AAAAGT T t aGT GG g t t a - - - CT AC g CT T GGc t t c g a aT CAAGa a a a a a t . . . . . . GACT T T T a

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AAACCT a c a - - - - . a t AGCT CT a a a - - - - - - AAACT T t t a - - - - - - AAGCT T a - - - - - - . a t AAACT T a t a - - - - - - AAAG t T t t a - - - - - - AAAT T Gc c aGGAA a t t

Q nad6 rrnS nad5 rrnS F rrnS

a a - - - - - - - - AGAA t a - - - - - - - t AAAGA t - - - - - - - - g c AGGA t a a - - - - - - a aAGGA t a - - - - - - - a aAGGA c . . . . . . . . . aAAGA t a a a g T T CC . . AAGA t

t t t t t t t

t t t t t t t

c g a c T T CT a a t a a . t t c g a c T CT T T - g a a . . t c g a aT CCT a . . . a t t t c g a aT CCT g - - - a a a . c g a aT CCT g - t t a a a t c g a c T CT T a - - - a a t t c g a aT CT T a . . . . . t t

. t t . at . . ata. caa . . . . . . ta. . t t .

. . . . . . .

. . . . . . .

aAGGT T T a c AGAGCT t t AAGT T T t aAAGT T T g aAAGT T T t t A c CT T T a t CAAT T T a

NC_002681 nad4 AGT GCT a - aAT GA t g t a - - - T CAT aCT T AA t t t c g a c T T AAG t t t aGGT g t t ACC . AGT ACT a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . ( ( ( . . . ) ) ) ) ) ) ) ) ) ) . Conservation: NC_005928 M

T T GAACT - - T GA t . a a a t a g a . c T T G t t AGGA t t g t t c aT CCT t - - - - a g c t AGT T CAA g

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

T AGGT t A a a - T AAGT G t t a - T T AAAC g t a - T T AAAC a a a - T T AAAC a t c - T T AAGC a t t a aT AAGT T c a a -

Q cox1 nad3 atp6 atp6 nad1 Q

-

-

. . . . -

. . . . -

. . . . -

- - - - - . - -at . . caa t - . gaa t - . . t a t aa . . . . tg. - - ac . . -

-

-

-

t GAAAA t g T GAAA t aT AAAA t aT AAAA t aT AAAA t aT AAAA c aT AAAA t

t t t t t t t

gt gt gt gt gt gt gt

t t t t t t t

a aT T T T C t a aT T T CA t a aT T T T A t a aT T T T A t a aT T T T A t a aT T T T A t a cTTTTA t

H

L1

a c a a a a - T t ACCT A g g t a a t - - t T ACT T A g t t a a a - - aGT T T AA a t a a a a - - aGT T T AA a t c a a a - - aGT T T AA a t g a a a a a aGCT T AA g t a g a a - t AGCT T A a g

cox3 nad1 nad4 A A A K

NC_002681 S2 T AGAGT c a aGCAT a t c a g a t g . AT GC aT AAAA c t g t t a t T T T T A a g a a t a c a aACT CT A g Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . ) ) ) ) ) ) ) . Conservation:

L1

NC_005928 W

GAT GGG g t aGT GT t c a a g aGCAC aT GT AA t t g t c g t T T ACA a a g g . c - - . . . . . . aT CCAT T t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AAGAA a t t aGT AT t a a a - - GT AC aT GAT T t AGGAA aT t aGT GT t . a t a aGCAC aT G t T T t GT AAAA a a aGT GT t g t t - - GCAT aT AT T T t AT AA t g A t aGT GT . a a t a - GCAC aT AT T T t AT AA t t A t g GT GT t a g t - - GCAC aT AT T T c T T T T AT T t aGT GT a a a a a aGCAC aT AT T T t AAGAAT T t aGT GT a t t t a aGCAC aT AT T T t

rrnS

. t g T T CT T a . A g T T CCT c . aT T T T AC a . T a t T T AT a . T t t T T AT a . AAT AAAA t . AGT T CT T g

nad2 I G I G W K

NC_002681 G AAAGGAT t aGT T T a a c c c aAAAC aT T AAT t t g t c a aAT T AA a g a t AAT a a t t AT T AT T CT T T a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . ( ( ( . . . . ) ) ) ) ) ) ) ) ) ) . Conservation:

nad3

nad4 nad1 M M M cox1 nad6

t t t t t t t


cob I I cox3 cox3 cox3 atp6 rrnL

c a aAAT CA t a a . . t t c a aAA t CA a a g t . t t c a aAAAT A a g g . . a t c a aAAAT A a a g . . t t c a aAAAT A a a g . . t t c a aAAAT A a a g a t t t c a aAAAT A t a g g a c t

- . - . - . a. a. - . - .

. . . . . . .

. . . . . . .

. . . . . . .

. . . . . . .

NC_005928 Q

t GAAAAGa a - - - - - - - - t c - - - t t T AGAG t t g c a a aCT CT A . . t c a a a a a a g . - - - CT T T T C t a

F

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AGAAAAT g aAT T AGAAAT C a t . . . t AAAGA a g a - - AAAAT T a a a - - CGA aT AC a t . . . AGAAAT t c c . . . CGaGGT t t a - - -

nad3 cox1 atp6 rrnS L1 rrnL nad4

rrnS nad3 Y M W nad5 cob

t . . . -

. . . -

g a a a a c AAT aAT T AT t t g c a a aAT AAT - . . . t a - - - - aAT CAT c t g c a a aGT GAT a c - - - a a - - - - c T T CAT t t g c a a aAT GAA - a c c t a - - - a t T AAGT t g g c a a aACT T A - . . t t a - - - t a t T T AA t t g c a a aT T AA t . . . . c t a - - - - aAT T AT t t g c a a aAT AAT . c t c c a a - - - t g T T AAA t t g c a a aT T T AA t c

. t . . t t t

- gaaa t aa agaa - - - - - aaaaaa t - - aaa t a t t aga - - - - - a t aa - - - - t - - - - - - - -

t -

- - AT T T T CT a - - GAT T T T T a - - c T CT T T t g g g g AAT T T T g - - GT A aT CGc - - t AT T T CT t - - c ACC c CGa

NC_002681 Y GAAGGAT t aGT A t a a t t a a t T AC aT AAGA t t g c a a g T CT T A - - . - g a a t t g - - - - - AT T CT T C t Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . . . . . . . ) ) ) ) ) ) ) . Conservation: NC_005928 C

T GT ACAA g aGT GT - - t g t t - GCAT aCAAAA t t t t g a c T T T T G - - t g g a t - T T GT ACA c

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

T GAAT t t t aGT GT a t a a t T GAAT T A a aGT GT g a a a t T T T T GAA a aGT GA - - a a t T T T T GAA t aGT GG . . . c t T T T T GAA g aGT GA - - a a t T GAAA t c t aGT GT - . - a t T GAAA t c t aGT GT - . - a t

N cox1 nad6 nad6 nad6 rrnS S2

a aGCAC t AT CAA t t - GCAC t AT CAA c t - T CAC aAAT AA c a - T CAC aGAT AA t t - T CAC aAAT AA t t aGCAC aAT T AA t t c GCAC aAT T AA t

t t t t t t t

t t t t t t t

t t t t t t t

g a aT T GGT g a aT T GAT g a aT T AT T t g a aT T AT C g a aT T AT T t g a t T T AAT g a t T T AAT -

t t -

a a g t t - t t AT T CA a a a g a t t T AAT T CA a t a t a t - T T CAAAA a t t t t t c T T CAAAA a a t t a t t T T CAAAA a t a g a t - t t T T T CA a a a g a a - a t T T T CA t

NC_002681 W T GT AT T a t aGT AT a g a c c c - GT AC aT AGAA a t t t g a aT T CT A - - a a g a c a aAAT ACA a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . ) ) ) ) ) ) ) . Conservation:

2

P R rrnS nad4l L2 nad4l nad3 N I

A


tRNAGlu Trichocephalida


tRNAGly Trichocephalida


tRNAHis Trichocephalida


tRNAIle Trichocephalida


tRNALeu1 Trichocephalida


tRNALeu2 Trichocephalida


tRNALys Trichocephalida

NC_005928 G

c AT GT CC t aGT GG - - - - - t g a t t . aT CAT aCCT CA t t t t c g aT GAGGa . g a a g a a aGGAT AT a t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

GAACT t Ga aGT GT GAACT T t t aGT GT AAAT AAT t aGT GT AAAT AT A t aGT GT AAAT AT a t aGT GT AAAT AA t t aGT GT AAGAAT a t aGT GT

-

-

-

-

-

. t -

- - t t - aa t - aa t - aa t - t t t aaa t aaa .

a aGCAC t AAGA t c . aGCAC t AAGA c t . aGCAT aAAGAA t . t GCAT aAGAAA t . aGCAT aAAGAA t . . GCAC aT AAAA t . aGCAC aAAGAA c

t t t t t t t

t t t t t t t

t t t t t t t

c a a t T CT T a a g a t a - . c a t t T CT T a a g t t a - . c a aT T CT T a g g a t - - . c a aT T T CT a g g . t a . . c a aT T CT T a g g a t t - . c a aT T T T A t a g a c a a . c a t T T CT T a g g . t a a .

L1

- C - AGT T T a - t AAGT T C t - AT T AT T T a t T AT AT T T t - aAT AT T T a - t T T AT T T t - c AT T CT T a

nad4 cox1 S1 L1 cob P L1

NC_002681 L2 GGT CT T c t g GT GA a t a t t c t c a t c aT CAC aACGAA a t t t c a aT T CGT a . g . t a c a t t AAGACT a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . ) ) ) ) ) ) ) . Conservation:

nad1

nad3 nad5 nad4 atp6 W L2 T

NC_005928 E

A t GGGGT t aGT AT a t t t a - GT AT t GCT AA t t t c c g aT T AGC - - - a g g t t - - - - - AT T CC - T a

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

CT AAT T C t aGT GT a a . a a . GCAC aT AAAA t CT AAC t A t aGT GT a a a a a - ACAC t T AAAG t CT AAT t t a aGT Ga a a - - - - c CAC aT AT AA t CT AT T T a t aGT GGa g t t a - CCAC t T AT GA c CT AAT t T a aGT GG - - c t c t CCAC aT AT AA t CT GAT T a a aGT GT - - t t a aACAC t AAT AG t t T T T AAT t aGT GT a a a t a - GCAT aCT T AG t

P cox1 D nad3 D P nad3

t t t t t t t

t t t t t t t

c c a aT T T T A c c a aCT T T A c c a aT T AT A t c c a aT CAT A c c a aT T AT A c c a aCT AT T c c a aCT AAG -

- aaga t - - - tat aaa t a aa t t a t - - - t ac - - aaa t - - agg t

t t t t t t

t t t t t

at - - - ga- -

t -

aGAAT T GGc - T t GT T AG t - t t AT T AGa - aAGAT AGa - A t AT T AG g - aAAT CAGa - AT T AAA t t

NC_002681 D GT CACT t t g GT GT a a t a t g GCAT g T AT GGc t t c c a aCT AT A - - - t g g t t t - - - - t GGT GAT a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . . . . . ) ) ) ) ) ) ) . Conservation: NC_005928 nad4

t AGT CT a c aGT T c t c t g t AAT t T T GGA a t g t g g g T CCAA - - a g g a t - - aAGACT t t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

CAGc A c A t a CAAT AAA a a T AAT AAA t t aAAT AAA t a T AAT AAA t a AAAT T T a - - T AT ACT a c a -

-

-

-

- aa - -at - - aaa -at t caag - - - - t aag -

-

-

-

aT T GAA a t t AAAGA t t t AT AAA t t aAT AAA t t t AT AAA t t a aT AGA t t a aA c AA a t


g a aT T CAA t a a c a a a g a aT CT T T - t a t a a t g a aT T T AT a a a a a a t g a aT T T AT a t a a a a t g a aT T T AT a a a a a a t g a aT CT A a - - - a a a t g g t T T aT a - - - - - - t -

H cox3 F cox2 cox1 nad2 nad2 I

K

- T t T aCT Ga - T T T AT T Ga - T T T AT T A t - T T T AT T a t - T T T AT T A a - aAAAT T T t - aAGT GT A a

G F T nad4 cox2 nad4l F

NC_002681 R GCT CT T T t aGT CT - a a g GGAC g T CGAA t t g t g g g T T CGG - - a g g a t t t AGGGGGC a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . ) ) ) ) ) ) ) . Conservation:

nad5

T M nad3 rrnS nad3 cob L1

A

NC_005928 nad3

AGT GT T A t t - - - - . . . . . . . t g . . - - - - g AT GCA g t g a t g t T GT AT c t t t g g g t t t c c - - - - T GACACT t

cox2

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

T CT T AAT a g - T CT T AAT t c . . T CT T AA t a g . . T CT T AA t a g . . T CT T AAT a g - aCT T AAT t a g . aCT T AAC g c Gc

R R rrnS D rrnS nad6 S1

S2 D rrnS cox2 rrnS L1 F

. . . . .

. . . . .

. . . . . . . . . . caa . . . agaa . . . t . aa t ag . . aa . aaa t aa t - - . ca. .

t a - . - - - - t T T T AA a t a a a t . - - - c T T T AA g t c a a . - - - - t T T AAA t t c a a . - - - - t T CAAA t t c a a . - - - - t T T AAA t t t c a g . - - - t T T AAA t t t g g . g c aC t T T T AA g t

ga t ga t ga t ga t ga t ga t ga t

a aT T AAA a t t a a a a a a aT T AAA g a a g t a a t a aT T T AA a t t a a a a . . a aT T T GA g t t a a a a . . a aT T T AA a t t a a a a - a aT T T AA a c t t t a a a a g T T AAA a t t t t a c a -

. . -

. . -

. . -

. . -

. . -

. . -

- AT T AAGA a - AT T AAGA a . t T T AAGA t . t T T AAGA t - AT T AAGA t aAT T AAGa t - GT T AAGc t

NC_002681 G T AAGT AGa aCCT A - - . . . a t t a a . T AGG g AT ACA g t g a t a g T GT AT - - t t t aGT G g c a aCACCT GCT T A a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . ( ( ( . . . . ) ) ) ) ) ) ) ) ) ) . Conservation: NC_005928 N

T CT AC c c t g GAG g a t t a - - g CT C aGT AAA t t t a g a aT T T GC t c a a a c a - - - - . - a aGT AGA g

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

aT T T AAA a aGT AT a c t a - - AT AC aT T ACT t AT T T AA t t aGT AT a a a a - - AT AC aT T ACT t T AAT CT t t aGT AT a a a a a - AT AC aGT AT T t T AAT C a t t aGT AT a a a a a - AT AC aGT AT T t T AAT CT a t aGT AT a t a a a - AT AC aGT AT T t AT CT T t a t aGT AT a t a a - - AT AC aT T ACT c T CT T A t G t aGT AT a t t t t aAT AC aT CGCT t

t t t t t t t

t t t t t t t

a g a aAGT AA a a a . . a g a aAGT AA a a a . t a g a aAAT AC a a a . t a g a aAAT GC a g a . t a g a aAAT AC a a a . t a g a aAGT AA a a a . t a g a aAGT GA a a a a t

ac - aaa t t - t t - t t - ta- t - - -

-

-

. . . . . . .

E

- T T T AAA c a - c T T AAAT t - t AGAT T A a - t aGAT T A a - aAGAT T A a - a t AAGAT a - T t T AAGA a

M Y I E T I E

NC_002681 N AT CAT T C t g GCA g a t a a a - g T GC a g T AAA t t t a g a aT T T A a a c a . t AC a t a aGT GAAT GAT a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . ( ( . . . . ) ) ) ) ) ) ) ) ) . Conservation:

A

nad5 cox1 A F C Y H

NC_005928 nad2

AT T AAC c t g GCA g - - a t . a a g T GC g T T GGA t t t a a g t T CCAG - - - a t a t t g a - - - - - c GT T AAT a

T

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

aT CT G t T t T T CT AT A t GAGAT t t t AAGAT t A t AAGAT t t t GAGAAT A t AAGAT aG t

P nad5 nad2 K nad2 E M

Y nad4 nad6 Q nad6 nad4l rrnL

aGT AT - a c t aGT AT - a a t aGT AT a a a t aGT AT a a a t aGT AT a a a t aGCAT - - a t aGCAT - a a t

. . . . t . .

a - AT AC aT T ACT t a - AT AC g T CACT t a aAT AC c T T AGT t a - AT AC t T T AGT t a aAT AC t T T AGT t a t AT GC aT T AGA t a aAT GC t T T AGT t

t t t t t t t

t t t t t t t

a a a aGGT AA a a a aGGT GA a a a aACT AA a a a aACT AA a a a aACT AA a a a aT CT AG a a a aACT AA -

-

-

aaa t aaa t aaa t aaa t aaa t aga t aga t

t t t t t t t

t t -

-

-

-

-

-

- A t CAGA a a - T AT AGAA t - t c AT CT T a - T t AT CT T a - t t AT CT T a - T AT T CT T a - T c AT CT T a

NC_002681 cox2 AT CAGT A t g GCA g - a c t . a - g T GC aAT T GA t t t a a g c T CAAT a c AAGA t t t c T T T T c T ACT GAT a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . ( ( ( ( . . . . ) ) ) ) . ) ) ) ) ) ) ) . Conservation: NC_005928 H

AGAAGG t t a t T GT a g g . t c - . GCA t a g AAGA t t t t t a aT CT T g c t g g . . a t a t . . . . t CCT T CT c

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AAAGAT t t a t T GT a a c . t AAAGGA a t . AGT G t a t . t t T T AGAT t t AT T T - - c a t c T T AGA c t t AT T T - - c t t T T T AGAT t t AT T T - - c t t t ACT A a c c aGT GT - - - t t T T T A g t G t aAGT . . g g c .

- - . GCA t g T T GAA t a a g CAT T aT CGAA c . a . GAAT aAT GAA t . a . GAAT aAT GAA t . a . GAAT aAT GAA t g a . GCAC t T T T AA t . . . . AT T aT T AGA t

t t t t t t t

t t t t t t t

S1 nad1 cob nad3 L2 nad4 nad5 N

AGT CAAA t aGCT T a a c c t t a . AAGC aCAAAT c t t t t a aAT T T Ga a g a . t GT a t c c ACT T T GACT a NC_002681 nad1 Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . ( ( . . . . ) ) ) ) ) ) ) ) ) . Conservation:

nad2

3

t t t t t t t

a aT T CAA a a g . . . . t a a . . . a aT T CGA - a g g . . . . a a . . . a aT T CAT c a g g . c a t a - - - a aT T CAT - a g g . g c t a - - - a aT T CAT - c a g . t t t a - - - a aT T AAA - a a g . . . t a a a a . a aT CT AA a g g a g a g a a . . . .

. t AT CT T T t . aT CCT T T t - AT CT AA t a - aT CT AA a a - AT CT AAA a . a aT AGT t a aT c aT AAA c

cob rrnL nad3 nad4l nad3 nad6 D

t t t t t t t

E

Q


tRNAM et Trichocephalida


tRNAP he Trichocephalida


tRNAP ro Trichocephalida


tRNASer1 Trichocephalida


tRNASer2 Trichocephalida


tRNAT hr Trichocephalida


tRNAT rp Trichocephalida

NC_005928 S2

T GAAGCT t aAGT T a . . g t t aGACT a aAGGA t t c a t g c T CCT c - a a g c g c g a a a g c - - AGCT T CA a

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AAAAGaT AAAAGT T t T AAGT T t T AAACT t T AAGT T T T AAAGT AT T AAG t

atp6 cox2 rrnL C rrnL T L2

t t t t t t t

aGACT a t a c a c aAGT C aT AAGA t aGACT a . . a t t aAGT C aT AAGA t aGACT a . . a a a aAGT C aT AAGA c aGACT a . . a t t aAGT C aT AAGA t aGACT a . . a t t aAGT C g T AAGA t aGACT a . . a t t aAGT C aT AAGA c aGACT a a a c c t aAGT C aT GAGA t

t t t t t t t

cat cat cat cat cat cat cat

a aT CT T A - a a a a t a aT CT T A - a g a t t a aT CT T A a a a t t t a aT CT T A a a a t t t a aT CT T A a a a t t t a aT CT T A a a a t t t a aT CT T A a g a t a t

aaat . at . a-

-

-

-

-

-

-

- A aCT T T T a - AGCT T T T c - AGCT T A t a - AGT T T A t a - GACT T A t a - GCT T T AA a - t CT T AAT t

NC_002681 F AGT AGT G t aAGCT a a g t t t aAGCT g T T GGG t t c a t a c CT CAA - - a t AT AC t t t GT GT CAT T AT T a Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . ( ( ( ( . . . ) ) ) ) ) ) ) ) ) ) ) . Conservation: NC_005928 atp6

AAGGAT t t aGT T T a g a g a - - - AAAC g T AGCT t t g a a g aAGCT A a a a g t - - - t GT CCT T a

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AT T T CT t a a AT CT CT t a a T GCT T AC a a CT T A c A c t a AT T g AT Ga t AGT CAT c a t AT T CT T Ga g -

Y W G L1 S1 cox2 H

-

-

-

aa - - - - - - - - - t . . . aaaag . . . t t tct . . . aaa . t ac - - - - t ccc a- - - - - - -

. -

. -

. -

. -

aAAAAA t aAAAAA t aT T AAA t aT T AAA t t T T AAA t aT T AAA t c t T AA a c

t t t t t t t

W H cox1 P nad5 R I

NC_002681 nad5 T CCCT T t t aGCT T a a g g t a - - AAGC aT GGGT t t g a a g aGCCT Ga g a t t t t - t GAGGGA g Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . ) ) ) ) ) ) ) . Conservation: T AAAAC t t aGT T T a a t - aGAAT a g AGAG t t t g g a aCT CT a a g g . t a a a . - c GT T T T G t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

T T AGA t T t aGT GT a a - - aGCAT aT T GT C t T T AGAAA a aGT GT a c - - t GCAT aT T AT C t t T AGAT a a aGT GT . . t a aACAT aT T AT T t t T AGAT a g aGT GT . a t - g ACAT aT T AT T t t T AGAT a a aGT GT . . t a aACAT aT T AT T t T AGAT T t t aGT GT c a a a aGCAT aT T AT T t T AGGGT g t aGT GT t a t a g GCAT aT T GCT t

G nad3 cox2 F cox2 E T

t t t t t t t

t t t t t t t

g g a aGAT AA a g g g g a aGAT AA a g g t g g a t AAT AA t g a g g a t AAT AA t g - g g a t AAT AA a g a g g a t AAT AA t g - g g a t AGT AA a g - -

t -

M

rrnS

a a - - - A t T CT AA a a a t t c T T T CT GA a a a t t - c AT CT A t a a a t t a aAT CT G t a a a t t - c AT CT A t a g a t t - t AAT CT A a g a a a - aGCCCT A a

L2 cox1 V V V G M

NC_002681 nad6 CAGAT T a t aGT T T a a t g aAAAT aT AAAG t t t g g g aCT T T A a g - - - - a t t a g AGT CT Ga Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . . ) ) ) ) ) ) ) . Conservation:

T

NC_005928 K

AT AGGGGa t a c - - - aGAAA t t t c t a aT T T C g - t t t aGC - . . t c t t . - - - GCCCCCT AT a

V

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AACCT T T - a a a t a aAAGAA t CACC t aGa a a a - - - GAAAA t T T ACT T A t t a a - - - aT GAA t T T ACT T A c t a a - - - GT GAA t T T ACT T A t a a a c a aAT GAA c AACT T CT - t a a t t aAT GAA t CT C c T A a a - - - t t t t T GAA t

A atp6 E nad2 F rrnS nad5

nad6 atp6 A rrnL nad2 nad5 I

t t t t t t t

t t t t t t t

c c c c c c c

t t t t t t t

a aT T CT T a aT T T T C a aT T CA a a aT T CAT a aT T CAT a aT T CAT a aT T CA c .

- - a t AGA . - t t t GAC . - t g t AGG . - t a aAGG . t t a a . GG . a t t t GGG g g c a t GA .

at . t . t gt at . . gt

. t t a a - T CT AAAGGT T a . a . a a - GT CT c t GGT G t a a t a . - CCT T AAGT AA a . . g a . - CCT T AAGT AA a . t t - - - CC . T AAGT AA a . . c a c . CCCGGAAGT T t . . a a c t T C t aT A aGAGa

NC_002681 cob AGAGAAGa c a t t - - T T AAGc t t c t a aCT T AA a g t a c T GGa a t . a c a a aCCACT T CT CT c Structure: ( ( ( ( ( ( ( . . . . . . . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . ( ( ( . . . . . . . . . ) ) ) ) ) ) ) ) ) ) . Conservation: NC_005928 M

T GACT t A t t a - - GAT AA t t t g a a aT T AT C t t t t GGC - - . . t t - - - - GCCT - AGT CA t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AGGAAAA t a a a - AT T AG t AAGGAA a a a t - - t T T GG t AGAAAT A - a a a - AT T AA t AGAAA t T - a a a c GT T AA t AGAAAT a a a t a aAT T AA t AGAAT aT t a t - - GT T AA t AGAAAAT t a t a - AT T AA t

cox1 A nad3 cob cob M nad5

t t t t t t t

t t t t t t t

g a a aCT AAT t a - - T GA t g a a aCCAA t - g t t GAA . . g a a aT T AAT t a g aT G - - g a a aT T AAT a a . . . G . . . g a a aT T AAT t a - - GA - - g a a aT T AAT a a t c AACC g a a aT T GAT t a a aGAA . .

rrnS

nad5

. . t a - - c t T CAT T T T CCT a a a t a . . . . T T C aT T CCT T a . - g a c a - - - CAT GT T T CT a a a t t a . . . . C . A t T T T CT a . . t a a t - - - T C aAT T T CT a . . t t a t . GGT T A - AT T CT t . g t g a . . . T T CAT T T T CT t

I nad2 cox1 nad1 nad1 nad1 Q

NC_002681 nad3 AAAGT T G - a a a g AAAAGc t t g a a aCT T T T c a a aT CAT Ga a . a . . CGT GACAACT T T t Structure: ( ( ( ( ( ( ( . . . . . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . ( ( ( ( ( . . . . . . ) ) ) ) ) ) ) ) ) ) ) ) . Conservation:

N

NC_005928 L2

AAAAGG t t aGCT - a a . t t a - . . - AGC aT T GAT t t t g t a aAT CAA - a g a t t t - c CCT T T T t

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

c T T GT T t t aGGT T a a a t t GT T t T a a aGGC . a a . t T T CCT g c t g . . . . . a c t c T CCC t T a t . . . . . a . t TTTCcTG t c . . . . . . . t T T CT T T A a aAGT T t a c t T CT T t A c t aGAT T a a a .

H nad2 H nad6 rrnL nad4 E

. a t . . GACC a aT T AT a a a . . . GCC aT T CAT a . t g . . - - - t T T T AT . g c a c - - - - t T T T AT a g t a . - - - - t T T T AT . - - . . AACT aT CT AT a a a . . GAT C g T T T AT

t t t t t t t

t t t t t t t

t t t t t t t


nad2

C

g a a a aT T T T T - t a . t a c a t AGAAAT a g a a a aT T T T T a a a . t a - - t AGGGAT a g a a a aT T T AA t t a a t a a - GT AAGCA t g a a a aT T T AA - t a t t - - - t T t T AAGc g a a a aT T T AA a a a a g g - - T AT aAAT g g a a a aT T T AA t t a t t a a a t AT GACT g g a a a a aT T A t - a a a t a a - T AAGAAT a

NC_005928 Q

N L1 H D D D S2 P

a aAT AA a a a g a t a - - t AACAA a a a aAT GAA - a g a t t t a aA c AAT t t a aAT AAA - a . t t a c . t aAGGAA t a aAT AAA - c . t t a a aA c GGGA t t a aAT AAA - a g t t t a aT A aGGAA t a aAT AGA - a a a t a t aT AAAGAA t a aAT AAA a a g t a a t - aT t AAGA a

NC_002681 nad4l GCT T T T A t aGT T T a a c c . c a . . GAAC aT AGAT c t t g t a aAT CT A a a g a a c c - T AAAAGC t Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . ) ) ) ) ) ) ) . Conservation:

V cox1 V cob rrnL L1 M P P

NC_005928 D

T CGGT c T t aGGT T - - - t c t GACT g CAAAC c t t c a a aGT T T G - a g g a t . . . . . . t . . . . . . A t GCCGA a

cob

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

A t T AGT T t aGGT T a t . t AT T AGA a t aGGT T a t g t AT T AAT t t a - G . C a c c . AT T AAT A a a - G . C a a c t AT T AAT A . aAGCT - - - t T c T AA t G t aAGT T a a t t AT T AT aT t aGGT T a a a t

. AAT T A c T a . c T CT AAT t . t AT T AAT a . T AT T AAT a . T AT T AAT a . C t T T A t Ga . A aAT AAT a

F rrnL cox2 nad1 E cox3 atp6

AT AGCT T t aAGT T a a g . t aAACT g T AAAC c t t c a a aGT T T G - a . t a t GGAC a t t g t GT T CAAGCT AT c NC_002681 Q Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . ( ( ( ( . . . . . ) ) ) ) ) ) ) ) ) ) ) . Conservation:

cox3

nad5 F nad1 cox3 C D atp6

t aAACC aT T GCT t t t g GACC aT CACT c t . aG . C a t CT ACT g t - - G . C a aT T ACT c t a aAGCT c T T ACT t t a aAACT aT T ACT t t t aGACC a aCGT T t t

4

t t t t t t t

c a a aAGCAA a a a t a t c a a aAGT GA a a . g t t c a a aAGT AG t a . t t t c a a aAGT AA c a a a t t c a a aAGT AA - a a . t t c a a aAGT AA - a a . t t c a a aAACG g a a g t t t

. . . . . . .

. . . . . . .

. . . . . . .

. . . . . . .

ac t aa t . . t . . t aa . . . t . . t

. . . . . . .

. . . . . . .

. . . . . . .

. . . . . . .

. . . . . . .


tRNAT yr Trichocephalida


tRNAV al Trichocephalida

NC_005928 nad3

T GACT AT a a a a a a . . . . . . aCT T GT c t g t a a aACAAG g t t c a g c c t a g c t aAT AGT CGa

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

A aAGGT T t t a a a - - GGAT T T C a a t g a t a A t GGT T T a a t a a . - c AGGT T T t a - t a t - AAGGT T T t a t a a - - A aGGT T t t a a a a . - AAAT C t T a a . . a c c t

L2 cox2 C A A L1 nad1

- - - - - - - - - - - - - - - - - - gca t

a t T AAT t t t GAAA t t T T AAT t t T T AAT t t T T AAT t aT T AAT t aT T AAG t

t t t t t t t

gt at gt gt gt gt gt

a a aAT T A t - - . - a g . a g aT T T C c t . . g a g t a a aAT T AA - a a a a . . a a aAT T AA - - - - . g . a a aAT T AA - - - a a . . a a aAT T AA g c t t a . . a a c CT T AA a a g t a . .

. . . . . . .

. . . . . . .

. . . . . . .

. . . . . . .

t t c AAT T T c T t a t - GAAAT T C a . t c AAGCT t T a t t c AAGCT T a t t t c AAACT T T t . t a t AGCT aT a . g t A t GGT T T a

aT A aCT T t a - g a t t - - - - - t T CAAA c t g t a a aT T T GA - . - a a t . . . . . a t aAAG g T A a t NC_002681 cox1 Structure: ( ( ( ( ( ( ( . . . . . . . . . . . . . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . . . . . . ) ) ) ) ) ) ) . Conservation:

A F cox2 nad5 nad5 nad5 atp6 cob C

NC_005928 S1

AAGGA t t t aGT T T . . a t c - . GAAC c T T T CT t t t a c a aAGAAA a a g t c - - - - t t T CCT T t

T

NC_008231 NC_008828 NC_008640 NC_008693 NC_008692 NC_008047 NC_008046

AT T T ACA t t - - - - . - - t g AT T aGc . . . T T T a c a t AT AT T CA a a - GT T . . . t T AT T C c A a t . GT A . a t t AT AT C c a a a - GT t . . . t AT AT T T t a a - GT T . . t t A g GGT T T - a - - - - . . g t

cob T nad4l nad4l nad4l cox2 rrnS

cox2 nad4 P P P cox3 rrnS

a a t . . . t a t T T AA c . a . AAA c aAT T AA t a a . AAC a t T AT AA c - - . T AC t t T AT AA t a a . t AC a t T AT AA t a a aAAC a t T AT AA t a a . - - - - aT T AAT t

t t t t t t t

t t t t t t t

a c a c T T AA t a a a t t t a a c a c T T AAT g a a . . . . . a c a t T T AT G - a t t t t a a c a c T T AT A - - - t t t a t a c a c T T AT A - a c t t a a a c a c T T AT A - a c a c t a a c a aAT T AA - a c t c a t -

- T GT AAAT t . t C aAAT g t - T GAAT AT t aT t GAAT A c - g aGAT AT t - t AAAT AT t - AAACC aT a

NC_002681 rrnS GAGC aT A . . GT AT . a a t t a . GT AT a c CT T Ga t t a c a aCAAGa a g g t . . . . . T A aGCT C t Structure: ( ( ( ( ( ( ( . . ( ( ( ( . . . . . . . ) ) ) ) . ( ( ( ( ( . . . . . . . ) ) ) ) ) . . . . . . . . . ) ) ) ) ) ) ) . Conservation:

5

rrnL

Suppl. Figure 2: Overlapping tRNALeu1 and tRNAHis in Thaumamermis cosgrovei. Both mitochondrial tRNA genes overlap for 14 nt (red). The anticodons are highlighted in bold.

tRNALeu1

tRNAHis

6

Suppl. Figure 3: Comparison of all armless mitochondrial tRNAs of Romanomermis nielseni. Anticodons are shown in bold.

tRNAAla

tRNAArg

tRNAAsn

tRNACys

tRNAHis

tRNAIle

tRNAP he

tRNAT hr

tRNAT yr

7