Fig. S1. Mature and precursor sequences and the predicted stem-loop structures of newly identified miRNAs in G. max. The mature miRNAs are in red. The actual size of the precursors may be slightly shorter or longer than represented.

1. gma-miR319g | UU CU UG A- UU AG- G AC UC AA AAAGCG GAGCU CUUCAGUCCA UAUGGG ACA UAAGA UCAAUU CU CCG UCAUUCA CA UGCUGAGUG A

||||| |||||||||| |||||| ||| ||||| |||||| || ||| ||||||| || ||||||||| CUCGA GAAGUCAGGU AUGUCC UGU AUUCU AGUUAA GA GGC AGUAAGU GU ACGACUCAU A ^ GG UC -- GA U- ACA G GU GA AA AGAAAG

2. gma-miR319h A| UU CUC U AG AG- G AC UC AA AGCG GAGCU CUUCAGUCCA AUGGG GAC UAAGAUUCAAUU CU CCG UCAUUCA CA UGUUGAGUGUA A ||||| |||||||||| ||||| ||| |||||||||||| || ||| ||||||| || ||||||||||| | CUCGA GAAGUCAGGU UGUCC UUG AUUCUAAGUUAA GA GGC AGUAAGU GU ACGACUCAUAU A C^ GG UCA U A- ACA G GU GA AG AAAU

3. gma-miR399d U A A - C U UA--| UCUCAU GGGCAAG UCUCC UUGGCAGGU GC CA UA GA UGCA \ ||||||| ||||| ||||||||| || || || || |||| CCCGUUU AGAGG AACCGUCUA CG GU AU CU ACGU A - A A U A U UUCA^ UUAUAA

4. gma-miR166g ----- C- A C-- -| U CCA C GGAC CAGG UUC UUC AGGC AUU GGAC CU A |||| |||| ||| ||| |||| ||| |||| || | UCUG GUCU AAG AAG UCCG UGA CCUG GA A AAAUC UA A AAU A^ C AC- C

5. gma-miR825b AA G .-CA| C CUC GAAGGU GAUGAUGA UGUUC G ||| |||||| |||||||| ||||| | GAG UUUUCA CUACUACU ACGAG G A- - \ --^ A (162 nt loop)

6. gma-miR396f AGG UUAAAA------| UGG CCACAGCUUUCUUGAGCUUCU GC UCC \ ||||||||||||||||||||| || ||| GGUGUCGAAAGAACUUGAAGA CG AGG A AUA UAGAAUAUAGAG^ UGG

7. gma-miR159e ------| CU GA UGGAGUGA AGGGAG CC A |||||||| |||||| || | AUUUCACU UUCUUC GG U CAUAAAUCAA^ C- AU

8. gma-miR172e C UUC A CA .-AACC .-G| A U AGUUUU AUG CU GCAGCAG GC GAGGCC UAUUGG AGCGA C |||||| ||| || ||||||| || |||||| |||||| ||||| | UUAGGA UAC GA CGUCGUC CG CUCCGG GUAACU UUGCU U C UAC - AA \ ---- \ -^ A U (11 nt loop) (28 nt loop)

9. gma-miR171i | AC - - AAAAUU CU- UUU UAUUG GCG GC UCAAUU ACAUGG GG \ ||||| ||| || |||||| |||||| || AUAAC CGC CG AGUUAA UGUACC UC U ^ -- A G ACUUC- AAU UAC

10. gma-miR157g U - U - U .-U| A GACAGAAG AUAGAGAGCACAGA GA UGA AUGCAUA UAUAU \ |||||||| |||||||||||||| || ||| ||||||| ||||| CUGUCUUC UAUCUCUCGUGUUU CU AUU UACGUGU AUAUA A A A C C C \ -^ U (20 nt loop)

11. gma-miR396g | A UAU AUCUUAU U CCA UUCCACAGCUUUCUUGA CUUCU GC AUC CU C ||||||||||||||||| ||||| || ||| || AGGGUGUCGAAAGAACU GAAGA CG UAG GA C ^ C UCC AAUUU-- - CCU

12. gma-miR166h UU CU G C UCUUCA- UU--| A GGGAAUG GUCUGG CGA GAC CU UCUUGAUC GUGUAG C ||||||| |||||| ||| ||| || |||||||| |||||| CCCUUAC CGGACC GCU UUG GA GGAACUGG CGUAUC U UU AG G U UACAUAA UGUU^ A

13. gma-miR854b

- AGGA - A GU GAGGUG AU .-GUGGAGGUGGU G .-G .-AGG| GGUGGUGGAGG

G GGN

AGGAG GAUAUGGAGG GGCC GCCGUGA GGUG G GCU AACCGCAACG GGAUAU GU GUGGUGG UUAUGGU UCAU

GUGGC \

||||| |||||||||| |||| ||||||| |||| | ||| |||||||||| |||||| || ||||||| ||||||| ||||

|||||

UCCUC UUGUGCCUUU UUGG UGGUAUU UCAU U CGA UUGGUGUUGC UUUGUG CG CAUCGCC GGUGCCA GGUG

UAUUG G

A GG-- U G UG AUA--- GU \ ------G \ - \ ---^ GAGAGGGUGGN

G GAG

(124 nt loop) (10 nt loop)(21 nt loop)

14. gma-miR319i A| UU CUC U AG AG- G AC UC AA AGCG GAGCU CUUCAGUCCA AUGGG GAC UAAGAUUCAAUU CU CCG UCAUUCA CA UGUUGAGUGUA A ||||| |||||||||| ||||| ||| |||||||||||| || ||| ||||||| || ||||||||||| CUCGA GAAGUCAGGU UGUCC UUG AUUCUAAGUUAA GA GGC AGUAAGU GU ACGACUCAUAU A C^ GG UCA U A- ACA G GU GA AG AAAU

15. gma-miR399c UG .-AA| AUUA U UAGGGCA UCUCUUUUGGCAGGU UGGUG CUUUGGA U ||||||| ||||||||||||||| ||||| ||||||| | GUCCCGU AGAGGAAACCGUUCA ACCAU GAGACUU A CG \ --^ C--- A (25 nt loop)

16. gma-miR482b AUU-| UC AGC UAUGGGGGG GGGAAGGAAUA CAUA \ ||||||||| ||||||||||| |||| AUACCCUCC CCCUUCUUUAU GUAU A ACAU^ C- AAA

17. gma-miR902 | U G- G C AAU UC GAAGA AGCA UG AUU UUG UUC U ||||| |||| || ||| ||| ||| | CUUCU UCGU AC UAG AGU AAG A ^ - AG G U AU- UU

18. gma-miR156h U A -- A CU --- .-AC| UG U A G CAGA AGAG GAGAG UU GUGAAC UU GC UC U | |||| |||| ||||| || |||||| || || || C GUUU UCUC CUCUC AA UACUUG AA UG AG C A - AC C UU GUC \ --^ GU U U (27 nt loop)

19. gma-miR396h U G UU AU .-UUUGUU -| U U GUU GGG GAGGC CUGUG GCC AC GC G ||| ||| ||||| ||||| ||| || || | CAA UUC UUUCG GACAC UGG UG UG C G G -- -- \ ------U^ C U (17 nt loop) (2nt in the loop) 20. gma-miR1088a U - - UC- C------A AAA- G UCU .-GAAUU| UG UA GU GC UCUC UCUU UGUCAA UC CAUG GGU AGAGG UUAG GG U|| || |||| |||| |||||| || |||| ||| ||||| |||| || CA CG AGAG AGAA ACAGUU AG GUAC UCG UUUCC AAUC UU A A C C UUU CAACCCC A GGUA G --- \ -----^ GU UG (16 nt loop)

21. gma-miR869b - AA UG .-UUCUGAUGGGAA -| U GAC UCAG GUUGA AUUAUGA GAUGG GGAA G ||| |||| ||||| ||||||| ||||| |||| UUG GGUC UAACU UGGUACU CUGUC UCUU G U G- -- \ ------A^ U (32 nt loop)

22. gma-miR1520e | C G CAUCC GUCACGUGU AUGUU UGA \ ||||||||| ||||| ||| CAGUGCACA UACAA ACU A ^ A G AAUCA

23. gma-miR1088c - UC G | CA GCA AGGA AGGGAGUA UGGU--GGAA \ ||| |||| |||||||| |||| |||| UGU UUCU UCUCUCGU GUCA CCUU A C C- - \ ^ CG (51 nt loop)

24. gma-miR1527b UAG UG -| A U AA GG UUCGACUUUG AAA UGACUUG GAGGUG AGGAU GU \ |||||||||| ||| ||||||| |||||| ||||| || GAGUUGGGAU UUU GUUGAAU UUCCAC UCCUA CG G AUU GU G^ A - A- AG

25. gma-miR167e U A -| UUC AAU GAAGC GCCA CAUGAUCUG UUACC \ ||||| |||| ||||||||| ||||| CUUCG CGGU GUACUAGAC AAUGG A A A C^ UCA AAG

26. gma-miR162d U C C UC C AA GU-| UU GCAG GGUU AUCGAUC UUC UG UC UG \ |||| |||| ||||||| ||| || || || CGUC CCAA UAGCUAG AAG AC AG AC U A U A CU U CA ACU^ AA

27. gma-miR1518b U A -- U -- .-UA| UU GUG UUGU GGUGAAU UCA GGC AACAU \ ||| |||| ||||||| ||| ||| ||||| CAC AACA UCACUUA AGU CCG UUGUG A A - UU U AG \ --^ CC (52 nt loop)

28. gma-miR156i | GA C AG A GAUAGA GCA AACCUG UC A |||||| ||| |||||| || UUGUCU CGU UUGGAC AG A ^ A- U CU G

29. gma-miR156g U - -| AU A UG AUU A GACAGA AGAG AGUGAGCAC GCU G GU UGUAUG G |||||| |||| ||||||||| ||| | || |||||| CUGUCU UCUC UCACUCGUG UGG C UA ACAUAC G A A U^ CG G GU --- G

30. gma-miR398d U U C AC- AUU ---| U CAGGG CG CCUGAGA CACAUGAA AG CAAAA UACAAGCA A ||||| || ||||||| |||||||| || ||||| |||||||| | GUCCC GC GGACUCU GUGUACUU UC GUUUU GUGUUCGU U C U U GAC AGU CCA^ U

31．gma-miR863 | UUU C GUUA GUUGAUGUUAAUA UGU AUU U ||||||||||||| ||| ||| | UAACUGUAGUUGU AUA UGA A ^ UCU U AGUU

32．gma-miR399b UG .-AA| AUUA U UAGGGCA UCUCUUUUGGCAGGU UGGUG CUUUGGA U ||||||| ||||||||||||||| ||||| ||||||| | GUCCCGU AGAGGAAACCGUUCA ACCAU GAGACUU A CG \ --^ C--- A (25 nt loop)

33．gma-miR403 C - -| UCU CAGGUU GUGCGUGAAUCUAAU CA AAGUU \ |||||| ||||||||||||||| || ||||| GUUCAA CACGCACUUAGAUUG GU UUCAA C A C C^ UUA

34．gma-miR171g C C AUGUAU - GG - CC C--| A GAUAUUGGC UGGUUCA UCAGAC ACCACGG CAC U UGUGU UUG UAGA A ||||||||| ||||||| |||||| ||||||| ||| | ||||| ||| |||| CUAUAACCG GCCGAGU AGUUUG UGGUGUU GUG G ACAUA AAC AUUU G U U GGUUU- A UU U A- AAA^ A

35．gma-miR529 CU- U C- -- UC .-AACCAC| U UACA GC ACC AC UC UUCUUCCAAGUCC GCUUU CUC \ || ||| || || ||||||||||||| ||||| ||| CG UGG UG GG AAGAAGGUUUAGG UGGAA GGG G GAC U UU CC UU \ ------^ C UACU (16 nt loop)

36．gma-miR413 | UUAA GAAGAGAG AUGCAGAAGAAGAGGG GAAG \ |||||||||||||||| |||| UACGUCUUCUUCUCUU UUUC A ^ UGA- AUGGGGAA 37．gma-miR1507c C------.-UA - .-GACGAAC| C UUUGUUCU U UUA UCAUU CCA CAUC GUCU CUAG GUUGA GCA GU \ ||||| ||| |||| |||| |||| ||||| ||| || AGUAG GGU GUGG CAGG GAUC CGACU UGU CA G GAGUUCA U \ -- U \ ------^ - UUGUU--- - UUU (38 nt loop) (130 nt loop)

38．gma-miR1507d U CGA A A A A----| CA CAGA UGUAUGGA UGAGAGAGGG AGAG GUA CGA \ |||| |||||||| |||||||||| |||| ||| ||| GUCU ACAUACCU ACUCUCUUCC UUUC CAU GCU G C CC- C C C AAAAG^ AA

39．gma-miR1088b C A .-AAA| CU G GGCGGAGGAG GAG AGCA UGUU GU A |||||||||| ||| |||| |||| || CUGUCUUCUC CUC UCGU ACAA CG A U - \ ---^ UU A (56 nt loop)

40. gma-miR171h | A CGC C AU UAU - CU GAU UUGG GG UCAAUCUGAG CG UUUAC UG U ||| |||| || |||||||||| || ||||| || CUA AACC CC AGUUAGGCUU GC AAAUG AC C ^ C ACU A CU CU- U AU

41. gma-miR167g U A -| GAU A GC GAA CUGCCA CAUGAUCU CUUUCC CA \ ||| |||||| |||||||| |||||| || CUU GACGGU GUACUAGA GAAGGG GU A A C C^ AUU A GA

42. gma-miR166f | UU - CU UCAAAGAGGA CAC AGGGGAAUG GGC UGG CGAGGCUUU GGUUCU U ||||||||| ||| ||| ||||||||| |||||| | UCCCCUUAC UCG ACC GCUUCGGAA UCAAGA G ^ U- G AG UA------ACG

43. gma-miR482c AUU-| UC AGC GGUAUGGGGGG GGGAAGGAAUA CAUA \ ||||||||||| ||||||||||| |||| CCAUACCCUCC CCCUUCUUUAU GUAU A ACAU^ C- AAA

44. gma-miR1510c A UG C- -| G GG GGGAUAGGUAAAACAA AC GCUGU AUAA U || |||||||||||||||| || ||||| |||| | CC CCUUAUCCAUUUUGUU UG UGAUA UGUU A A GU AU U^ A

45. gma-miR479 | A CGC C AU UAU - CU AGUGAU UUGG GG UCAAUCUGAG CG UUUAC UG U |||||| |||| || |||||||||| || ||||| || UCGCUA AACC CC AGUUAGGCUU GC AAAUG AC C ^ C ACU A CU CU- U AU

46. gma-miR1508c A A -| UUACA C CAACUGCUAUUCCC UUUCUA ACC UUG CGAG \ |||||||||||||| |||||| ||| ||| |||| GUUGACGAUAAGGG AAAGAU UGG AAC GUUC A G C U^ UA--- U

47. gma-miR167f U| CA C G AG- CA-- C GAGGCUGU CAGCAUGA CUA UC GGUUAG CU U |||||||| |||||||| ||| || |||||| || | CUUCGACG GUCGUACU GAU GG CCAAUC GA U A^ -- A - AAA UCUC G

48. gma-miR474 U G UACAA .-CCGU UG G UA--| G CUUAUUA GAC CCGGUAA GUGUU GU CCCU AGG A ||||||| ||| ||||||| ||||| || |||| ||| GAAUAGU UUG GGUCGUU UAUAG CG GGGG UCC G G ------\ ---- GU G UAGG^ C (20 nt loop)