Supplementary Material
Identification of soybean microRNAs and their targets
Baohong Zhang1,*, Xiaoping Pan2, Edmund J. Stellwag1
1 Department of Biology, EastCarolinaUniversity, Greenville, NC27858
2 Department of Chemistry, WesternIllinoisUniversity, Macomb, IL61455
Fig. S1 Schematic representation of the miRNA gene search procedure for identifying soybean homologsbased on established Arabidopsis miRNAs
Fig. S2 Predicted hairpin secondary structures of the 74 soybean miRNAsidentified in this study.
Fig. S1 Schematic representation of the miRNA gene search procedure for identifying soybean homologsbased on established Arabidopsis miRNAs
gma-miR156a
- -| au a ug auu a
ugacagaagagagugagcac gcu g gu uguaug g
acugucu ucuc ucacucgug ugg c ua acauac g
a u^ cg g gu --- g
gma-miR156b
-| agaacca ug
gug uuucu c c uguu a
cacagaga g gacag u
g^ -ga- aa- uu
gma-miR157a
ag uua uuccg ag u ac u ca .-aaaa| caga u
gc ucucu uuucug ca gcau uca ucacag uc ugca ucc g
cg agaga gaagac guugug agu aguguu ag acgu agg a
ca --- ua--- a- - a- u uc (34 nt loop) uag- u
gma-miR157b
u - u u - a -| gaa
ugacagaagauagagagcac ga ga uga aug cau a
acugucuucuaucucucgug uu cu acu uac gua g
u g u c c c g^ agg
gma-miR157c
a| c aaag g cauucc
ugacagaagauagagagcac ga ugagaugc \
acugucuucu aucucucgug cu acuuuacg c
a^ - acua - uacuuu
gma-miR157d
u - u - u --| auaauauauagc g
ugacagaagauagagagcacaga ga uga augcaua uuau ag g
acugucuucuaucucucguguuu cu auu uacgugu agua uc a
u a c c c ua^ guac------a
gma-miR157e
a u aag guaag .-acaauucaucaug| uc
ugacagaagauagagagcaca ga augc agu \
acugucuuc uaucucucgugu cu uacg ucg c
a - cua acua- (16 nt loop) uc
gma-miR157f
u a- a a-| g u u g
ugacaga gagagaggcaca cccgg aa ggc aaag a
acugucu uucucuc cgugu ggguu uu ccg uuuc g
u cc c ga^ g u - u
gma-miR159a
ga uu aucu ---- ug u g c uc uu -| ucaaua
uggagcuccuu aguccaa gagg uacu ggg aau gagcu cuuag uaugga ccacag cuacc ca a
aucucgaggga uuagguu uucc auga ucc uua uucga ggguc auaccu gguguu gaugg gu g
ag uc aauu uauu gu c g u uc cu u^ uuucgu
gma-miR159b
g g -- uc a ug ug aa--- - aa - ug (24 nt loop) a- aug- cg ---- aaucaa - c
uuugauuaaggga ga cuaccu ucu u u------ggaga ga cag cc cu ca acuc ccuugg ugu ug ccaugg gcaga gaa a
aaa uugg uuccuu uu ggugga agg a a ucucu cu guc gg ga gu ugag ggaacc aca ac gguacc cgucu cuu a
g g gu gu - gu gu (23 nt loop) guucc c ca a gu ------aa agua ug ucua guucc- a g
gma-miR160a
c c c c a
ugcuggcuccuguaugccauuuguagag ucau ga g
acg accgagg guaugcgguagguguuuc agua cu c
a a c a a
gma-miR160b
c| cccu g a
ugcuggcu guaucc g
ac gaucga caug gg c
a^ cuuu a a
gma-miR160c
ugcug ugu c gaa| auu u aaugg aauag
c gcuccc augccu ca cu gu aucuuc uaca \
g ugaggg uacgga gu ga cg uggaag augu a
uu- gu u-- a aa-^ gau u aguua gguug
gma-miR162a
c c uc c aa gu-| uu
cuggaugcag gguu aucgauc uuc ug uc ug \
gaccuacgucccaauagcuag aag ac ag ac u
u a cu u ca acu^ aa
gma-miR162b
| u a ga a gu u a uu
cugg ugcag gguuuaucgauc uuc ug uc g ug \
gaccacgucccaaguagcuag aag ac ag c ac a
^ u g ag g uu - a aa
gma-miR163
caa ga ug- u ug uag u a| uguugg g au- aaag ug a
aagag cuu aacug aga ug ugc ac gugcag ugaaagga uga c a \
uucuc gag uug au ucu au acg ug uacguu acuuucuu acu g u a
cua g- ucg - gu ua- - -^ ------auu ca-- gu a
gma-miR166a
| uu - cu ucacaaagga a gu
ggggaaug ggc ugg cgaggcuuu gguuc ca \
ccccuuac ucgacc gcuucggaa ucaag gu g
^ u- g ag ua------ag
gma-miR166b
ga uu cu - ggagg------.-agag| a
ggaaug gucugg cgag gucau aagagg uacug g
ccuuac cggacc gcuc uagua uucucc gugac a
cc uu ag u aaaaagacacacacacaa (22 nt loop) u
gma-miR166c
uu cu g c ucuuca- uu--| a
ggggaaug gucugg cga gac cu ucuugauc guguag c
ccccuuac cggacc gcu uug ga ggaacugg cguauc u
uu ag g u uacauaa uguu^ a
gma-miR166d
| c g a gauauaucacuucaccauacucauaucuucacaaacu aga
ggggaaug agu uggucc aggagau cauc \
ucccuuacucgaccagguccucug guag u
^ u g c -----uauuauacguauauaauguuuaaua------acu
gma-miR166e
uu c gu cuaugcau uuuu - aa---- u uu uc
ugggaaug guuugg ucgag aa ggucuuaa guuca ucuuugaagcuuu uuua ggg ucga \
gcccuuac cggaccggcuc uu ucggaguu uaggu ggaaauuucgaaa aagu ccc aguu u
uu a ------u--- u gaaaca u u- uc
gma-miR166f
uu - cu ucacaa ga a gu
ggggaaug gg cugg cgaggcuuu au gguuc ca \
ccccuuac ucgacc gcuucggaa ua ucaag gu g
u- g ag ------ag
gma-miR166g
a uu c - ggaggagg-- a -----ag------a
g ggaaug gucugg ucgag gucau aggagg guag uacug g
cccuuac cggaccggcuc uagua uucucc cauu gugac a
c uu a u aaaaaacaca - uaaagguaaccuuugaaa u
gma-miR167a
a - -| cuuu ggga ga
ugagcugccagcaugaucuag gguuagu gc g
acu cga cg gucguacuggauc ccaaucg ug a
c u u^ acuc ---- au
gma-miR167b
u g ag uuc
ugaagcgccacaugaucug uuuacc \
acuucg cggu guacuagac gaaugg u
u - aa uua
gma-miR168
c u a uc - aa--| ga
ucguuggugcaggcggga ccgguuu gcg cgg ug n
agu aacuacguuc gcccu gguuaag cgc gcc gc g
c c a c- g gcug^ ga
gma-miR169a
--c- g c ccga-| cuu
cag caagaugauug uaaauu u
guu guuu uacu aac guuuaa c
aacu g u uuuca^ ucu
gma-miR169b
c gu uuauu --| cu g
gagccaagagacuugccggcg auu ug cau u
u ucgguuu u uugaacggccgu ugg ac gua u
a g g uccuu cc^ uc c
gma-miR169c
| au uu caaguga ca a
agccaagg gacuugccggca agc augag ucauauauauauauau u
ucgguucc uugaacggcugu uug uacuc aguauauauauauaua a
^ gg uc ------u
gma-miR169d
c g uuauu --| cu g
agccaagaugacuugccggcg auu ug cau u
ucgguuu uguugaacggccgu ugg ac gua u
a g uccuu cc^ uc c
gma-miR169e
ga caa aga -- c .-cucaacacgaa -| aaaccagaac
ggguaa uca ucc guuc uauguua auag guc aga \
uccguu agu agg cgag auauaau uauc cag ucu a
g- --- aac ua - (140 nt loop) a^ acaccacaaa
gma-miR169g*
| au uu caaguga ca a
agccaagg gacuugccggca agc augag ucauauauauauauau u
ucgguucc uugaacggcugu uug uacuc aguauauauauauaua a
^ gg uc ------u
gma-miR171a
| uc a au u
gauauugg cgguucaau agaaagca gcucaaaa \
cuauaacc gccgaguuauuuuuugu uggguuuu g
^ gu c cc u
gma-miR171b
c u g-| aagau
gguauuggcgug cucaauu gaa acaugguu g
cuauaacugcgcgaguuaa uuu uguaccga a
c u aa^ ccaaa
gma-miR171c
| uc a au u
gauauugg cgguucaau agaaagca gcucaaaa \
cuauaacc gccgaguuauuuuuugu uggguuuu g
^ gu c cc u
gma-miR171d
a c a - ga-| a a
gauguuggug gguucaauc g aga cg uuuac ugu g
cuauaaccgcccgaguuag c ucu gc aaaug acg a
g a - a aua^ - a
gma-miR172a
a ug-- c-| ag -- g g uugau auc
auguagcaucaucaagauuc ca caag gc guggu gg ugg ac gca \
uacgucguaguaguucuaag gu guuu ug uaccg cc acc ug cgu u
a caag uc^ ga aa g g u---- gaa
gma-miR172b
a - u- a-| g acuau u auc
auguagcaucaucaagauuc caug caaa ga ggugggu gg ga gca \
uacgucguaguaguucuaag gugu guuu cu cuaccua cc cu cgu c
a a uu gg^ a gu--- - gaa
gma-miR172c
a -- gau -| ca ga g ua ug guag
aga uccugau gcug gcaga ac augg c gg c
uc u gggguua cg ac cguuu ug uacc g cc a
c ga acc c^ -- g- - -- gu aguu
gma-miR172d
ggaa --- u--- u --| gcaag - -- uaa-- accu ac
uccug auga gcgcaguagaga agggugga aguugc ccu gcca gg ugg \
aggau ugcu ug cguuaucucu uccuaccu ucgacg ggg cggu cc acc u
agaa aga ccuu u uc^ ----- a ca uuaac gu-- gu
gma-miR319a
| a uu cuc u ag ag- g ac uc aa agcg
ag gagcu cuucagucca auggg gac uaagauucaauu cu ccg ucauuca ca uguugagugua a
uccucga gaagucaggu ugucc uug auucuaaguuaa ga ggc aguaagu gu acgacucauau a
^ c gg uca u a- aca g gu ga ag aaau
gma-miR319b
| cc c uu uaacga uu ugaau ac --- acaca g aa
aaggagcuuc ucag cca cauggaga aaga ggguugc ua ugcua gcuc uucauucauacaaua uauuc \
uuccucgagg agucggu gugucucu uucu cccaacg au augau ugag aaguaaguguguuau auggg u
^ aa a uc ------uuau- cu aua ggcg- a au
gma-miR319c
g gu g augau c ua g uu gau uc uu aac
uuggaguucccu cacuccaa cu aaaggau gguaaac uc cu cuag caug acc ugacuuc aac \
gaccucgagggagugagguu gg uuuucua ccauuug ag ga gguc guac ugg acugaag uug a
a au - guu-- - ua g cc guu ga c- cgu
gma-miR394a
uc - cuacucucucuc| ca
uuggcauuguccaccucc acuuc ugagc \
aacugu a acggguggagg ugaag gcuug c
c u u u------^ ua
gma-miR394b
uc acuucu-| cc
uuggcauuguccaccucc ugg c
aaccgu a auagguggagg auc u
c u cucaugc^ ua
gma-miR395
| g uu agu
gaguuccucugaacgcuucau uga ggcu \
cucaaggggguuugugaagua guu ccgg u
^ - u- aua
gma-miR396a
c uc-| ------u uuu u
uuccacagcuuuuugaacugca caa agagu cc gca g
agggugucgaaaaacuuggcgu guu ucuca gg cgu c
u uuu^ cuaaacccucau c uac a
gma-miR396b
c a c aaa| gauuugggagua g aug u
uccacagcuuuuugaacgca caa agagu cc gca g
a ggugucgaaa aacuug cgu guu ucuca gg cgu c
a g a ag-^ ------a aaa a
gma-miR396c
| a uau aucuuau u cca
uuccacagcuuucuugacuucu gc auc cu c
agggugucgaaagaacu gaaga cg uag ga c
^ c ucc aauuu-- - ccu
gma-miR396d
c agg uuaaa--| - gga
uccacagcuuucuugagcuucu gc auc cu g
a ggugucgaaagaacuugaaga cg uag ga g
a aua uagaaua^ a ggu
gma-miR398a
g| a a cu ug a gc uc
gagg guga ucugagaacacaagg gguu c cu uauauca \
uucccacuggacucuuguguuuc uuaa g ga auauggu u
-^ c - au gu - -- ua
gma-miR398b
u u c ac- auu ---| u
caggg cg ccugaga cacaugaa ag caaaa uacaagca a
gucccgcggacucuguguacuu uc guuuu guguucgu u
c u u gac agu cca^ u
gma-miR399
-| guu ca aa
ugccaaagga uug agcu \
gugg uuuucu agc ucga a
a^ ac- a- aa
gma-miR408a
-| c g c a g u aaaugguaaagugagaauga
gcu gggaa aggcag gca ga ug agcua caacaga \
cggcccuuuccguccgu cu gc ucggu guugucu a
u^ c a a c a - agagagagagagagagagga
gma-miR408b
| a c a ga u caa g- aagaa ug
gc ggggaa aggcag gcaug uggagcua caaca uauu uc ac \
cgucccuuuccguccguac gucuuggu guugu auaa ag ug a
^ g c a uc - --- ag gagag ag
gma-miR414
a uc - ca-- cc cuccaaacu| ccccc ug- .--- --cuccc------uaaac- u aca- -- cuug
auucuuca auccucgu uccu agau cau ugaa gc cag ca gau gcaugggg aauaau u
ua agaagu uggg ggcg agga ucua gua acuu cg guc gu cua uguauccc uuguua c
a -- u uuca cu cuacuucu-^ acu-- cua auucugaaguuccucagcc uaccuu u auac ag uucu
gma-miR415
- - - a- g a a-| ga
aacagaggagaa caaaagc uu u
uug ucuc uuc uu gu uuu cg ag a
u a a ga g a ag^ au
gma-miR426
ca| uc gga aaa ga g
uaagga gaau caa gguugca ucu g
auuccu uuua guu ccgaugu gga c
cc^ c- aag gaa ag a
gma-miR447
cc a- ug---| gau
guaugga ag uguuuugu aug \
uaugucu uc acgaaaua uac c
-- gc cauaa^ agu
gma-miR779
aa uu-| u uuuuuu
ugauugg au ccuu ccuuc u
acugauu ua ggaa gggag u
gg uuu^ u ccuucg
gma-miR781
| au gcu - ug g u
ucuuuc uguau gagagcucua gu u ug g
agaaag acaua cuuuugagau ca g ac g
^ -- agu u gu - u
gma-miR824
u| cca a ucucuguuugu
aga uuuguggaacagaa \
ucu agauac cuuguuuu u
u^ ucc - cuacuauuguu
gma-miR825
u aa g c- ucc ------uauuu u .-ggugg| ----- uc---- caa
ucuc gaaggugaugauga augu ggag agcaa gacag gu gggcc auuaga ugcauccgag g
a gag uuuuca cuacuacu uaua ccuu ucguu cuguc ca ucugg uagucu acguagguuu c
u a- - uc --- uaaauuucg uccuu - (43 nt loop) aguua ucaaac uac
gma-miR830
-a aaa u acauacacuuauguguaaa ua
auu uuucuca agua uuagcga gguga u
uaa gaagagu uuauaauuguu ucauu u
aa c-- c cuuaaguggguaacuauacccgag ca
gma-miR854
a aug gagg-- u-| c
gaagggau gaggag augac auuuggaa g
cuuc ccua cuccuu ugcug uagaccuu u
- ga- gacagg cu^ g
gma-miR860
| aucu c gcu auaa a c - a agca
gcuca ucc aucca cau cu cua aggua ug uc \
cgggu agguaggu gua ga gau uucau ac ag u
^ auc- u aac aca- - u u - acaa
gma-miR862
uu - uaa u---- aa-- - -- .-cacaa-- a
cugu ugcucc ccuguu gcc uaucau gcu uagaa uggca gga u
ggug acgaggggauaa cgg guagug ugg aucuu accgu ccu u
u- u ca- ucuuc gggg u uc (92 nt loop)^ u
gma-miR865
c| cug gcu gg- g guugc
uugg agauu guuaa cu uucuugcu \
aauu ucuag uaauu gg aggagcgg u
a^ aa- guu gua a ucuag
gma-miR869
| u u g g
ucucaggucaaucugguguua a
agggu ccg guua gguuguggu g
^ u - a u
gcl-miR396a
c a c aaa a u ggga--| aga c
uccacagcuuuuugaacgca ca gg gu gca gugc a
aggugucgaaaaacuugcgu gu uc ca cgu uacg u
a g a ag- a u aggaar^ acg g
gcl-miR396b
c uccau| a uccuur ugca c
uuccacagcuuuuugaacugca ag gu gca ugc a
agggugucgaaa aacuuggcgu uc ca cgu acg u
u uuugu^ - cacccu ucuc g
gso-miR169a
c| au uu caaguga ca a
agccaagg gacuugccggca agc augag ucauauauauau u
ucgguucc uugaacggcugu uug uacuc aguauauauaua a
a^ gg uc ------u
gso-miR169b
gc| au uu caaguga ca a
agccaagg gacuugccggca agc augag ucauauauauau u
ucgguucc uugaacggcugu uug uacuc aguauauauaua a
ua^ gg uc ------u
gso-miR169g*
| au uu caaguga ca a
agccaagg gacuugccggca agc augag ucauauauauau u
ucgguucc uugaacggcugu uug uacuc aguauauauaua a
^ gg uc ------u
Fig. S2 Predicted hairpin secondary structures of the 74 soybean miRNAsidentified in this study. Mature miRNA sequences are in red color. The length of the accurate miRNA precursors may be slightly longer than what is presented here
1