<p>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.</p><p>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</p><p>||||| |||||||||| |||||| ||| ||||| |||||| || ||| ||||||| || ||||||||| CUCGA GAAGUCAGGU AUGUCC UGU AUUCU AGUUAA GA GGC AGUAAGU GU ACGACUCAU A ^ GG UC -- GA U- ACA G GU GA AA AGAAAG </p><p>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 </p><p>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 </p><p>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 </p><p>5. gma-miR825b AA G .-CA| C CUC GAAGGU GAUGAUGA UGUUC G ||| |||||| |||||||| ||||| | GAG UUUUCA CUACUACU ACGAG G A- - \ --^ A (162 nt loop)</p><p>6. gma-miR396f AGG UUAAAA------| UGG CCACAGCUUUCUUGAGCUUCU GC UCC \ ||||||||||||||||||||| || ||| GGUGUCGAAAGAACUUGAAGA CG AGG A AUA UAGAAUAUAGAG^ UGG </p><p>7. gma-miR159e ------| CU GA UGGAGUGA AGGGAG CC A |||||||| |||||| || | AUUUCACU UUCUUC GG U CAUAAAUCAA^ C- AU </p><p>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)</p><p>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 </p><p>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)</p><p>11. gma-miR396g | A UAU AUCUUAU U CCA UUCCACAGCUUUCUUGA CUUCU GC AUC CU C ||||||||||||||||| ||||| || ||| || AGGGUGUCGAAAGAACU GAAGA CG UAG GA C ^ C UCC AAUUU-- - CCU </p><p>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 </p><p>13. gma-miR854b</p><p>- AGGA - A GU GAGGUG AU .-GUGGAGGUGGU G .-G .-AGG| GGUGGUGGAGG</p><p>G GGN </p><p>AGGAG GAUAUGGAGG GGCC GCCGUGA GGUG G GCU AACCGCAACG GGAUAU GU GUGGUGG UUAUGGU UCAU</p><p>GUGGC \</p><p>||||| |||||||||| |||| ||||||| |||| | ||| |||||||||| |||||| || ||||||| ||||||| ||||</p><p>|||||</p><p>UCCUC UUGUGCCUUU UUGG UGGUAUU UCAU U CGA UUGGUGUUGC UUUGUG CG CAUCGCC GGUGCCA GGUG</p><p>UAUUG G</p><p>A GG-- U G UG AUA--- GU \ ------G \ - \ ---^ GAGAGGGUGGN</p><p>G GAG </p><p>(124 nt loop) (10 nt loop)(21 nt loop)</p><p>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 </p><p>15. gma-miR399c UG .-AA| AUUA U UAGGGCA UCUCUUUUGGCAGGU UGGUG CUUUGGA U ||||||| ||||||||||||||| ||||| ||||||| | GUCCCGU AGAGGAAACCGUUCA ACCAU GAGACUU A CG \ --^ C--- A (25 nt loop)</p><p>16. gma-miR482b AUU-| UC AGC UAUGGGGGG GGGAAGGAAUA CAUA \ ||||||||| ||||||||||| |||| AUACCCUCC CCCUUCUUUAU GUAU A ACAU^ C- AAA </p><p>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 </p><p>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)</p><p>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)</p><p>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)</p><p>22. gma-miR1520e | C G CAUCC GUCACGUGU AUGUU UGA \ ||||||||| ||||| ||| CAGUGCACA UACAA ACU A ^ A G AAUCA </p><p>23. gma-miR1088c - UC G | CA GCA AGGA AGGGAGUA UGGU--GGAA \ ||| |||| |||||||| |||| |||| UGU UUCU UCUCUCGU GUCA CCUU A C C- - \ ^ CG (51 nt loop)</p><p>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 </p><p>25. gma-miR167e U A -| UUC AAU GAAGC GCCA CAUGAUCUG UUACC \ ||||| |||| ||||||||| ||||| CUUCG CGGU GUACUAGAC AAUGG A A A C^ UCA AAG </p><p>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 </p><p>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)</p><p>28. gma-miR156i | GA C AG A GAUAGA GCA AACCUG UC A |||||| ||| |||||| || UUGUCU CGU UUGGAC AG A ^ A- U CU G </p><p>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 </p><p>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 </p><p>31．gma-miR863 | UUU C GUUA GUUGAUGUUAAUA UGU AUU U ||||||||||||| ||| ||| | UAACUGUAGUUGU AUA UGA A ^ UCU U AGUU </p><p>32．gma-miR399b UG .-AA| AUUA U UAGGGCA UCUCUUUUGGCAGGU UGGUG CUUUGGA U ||||||| ||||||||||||||| ||||| ||||||| | GUCCCGU AGAGGAAACCGUUCA ACCAU GAGACUU A CG \ --^ C--- A (25 nt loop)</p><p>33．gma-miR403 C - -| UCU CAGGUU GUGCGUGAAUCUAAU CA AAGUU \ |||||| ||||||||||||||| || ||||| GUUCAA CACGCACUUAGAUUG GU UUCAA C A C C^ UUA </p><p>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 </p><p>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)</p><p>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)</p><p>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 </p><p>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)</p><p>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 </p><p>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 </p><p>42. gma-miR166f | UU - CU UCAAAGAGGA CAC AGGGGAAUG GGC UGG CGAGGCUUU GGUUCU U ||||||||| ||| ||| ||||||||| |||||| | UCCCCUUAC UCG ACC GCUUCGGAA UCAAGA G ^ U- G AG UA------ACG </p><p>43. gma-miR482c AUU-| UC AGC GGUAUGGGGGG GGGAAGGAAUA CAUA \ ||||||||||| ||||||||||| |||| CCAUACCCUCC CCCUUCUUUAU GUAU A ACAU^ C- AAA </p><p>44. gma-miR1510c A UG C- -| G GG GGGAUAGGUAAAACAA AC GCUGU AUAA U || |||||||||||||||| || ||||| |||| | CC CCUUAUCCAUUUUGUU UG UGAUA UGUU A A GU AU U^ A </p><p>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 </p><p>46. gma-miR1508c A A -| UUACA C CAACUGCUAUUCCC UUUCUA ACC UUG CGAG \ |||||||||||||| |||||| ||| ||| |||| GUUGACGAUAAGGG AAAGAU UGG AAC GUUC A G C U^ UA--- U </p><p>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 </p><p>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)</p>