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Table 3 Identified targets of known miRNAs in soybean

From: Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

miRNA

Target gene

Target annotation

Class

Abundance(TP10M)

cleavage site(nt)

target site location

gma-miR156

Glyma04g37390#

SBP domain protein

I

39

938

5'UTR

 

Glyma06g17700#

SBP domain protein

I

39

1185

CDS

 

Glyma05g00200*

SBP domain protein

I

42

1202

CDS

 

Glyma04g32070*

SBP domain protein

II

42

130

3'UTR

 

Glyma17g08840*

SBP domain protein

I

42

1011

CDS

 

Glyma05g38180#

SBP domain protein

I

33

1356

CDS

 

Glyma08g01450#

SBP domain protein

I

33

1154

CDS

 

Glyma18g00890

SBP domain protein

II

75

249

CDS

 

Glyma12g27330

SBP domain protein

II

17

621

5'UTR

 

Glyma11g36980

SBP domain protein

II

47

1223

CDS

 

Glyma02g30670

SBP domain protein

I

109

688/689

CDS

 

Glyma18g36960

SBP domain protein

I

14

723

CDS

 

Glyma02g13370

SBP domain protein

I

173

1219/1220

CDS

gma-miR159

Glyma15g35860#

MYB family transcription factor

II

27

937

CDS

 

Glyma13g25720#

MYB family transcription factor

II

27

838

CDS

 

Glyma20g11040

MYB family transcription factor

I

17

918

CDS

gma-miR160

Glyma11g20490#

Auxin response factor

II

134

1510

CDS

 

Glyma10g35480#

Auxin response factor

I

134

740

CDS

 

Glyma12g08110#

Auxin response factor

II

134

1501

CDS

 

Glyma13g20370*

Auxin response factor

I

177

1670

CDS

 

Glyma10g06080*

Auxin response factor

I

177

1355

CDS

 

Glyma13g02410

Auxin response factor

I

74

1280

CDS

 

Glyma14g33730

Auxin response factor

I

29

1184

CDS

 

Glyma19g36570

Auxin response factor

II

807

652

CDS

 

Glyma04g43350

Auxin response factor

II

43

1337

5'UTR

 

Glyma13g40030

Auxin response factor

II

67

1277

CDS

 

Glyma20g32040

Auxin response factor

I

19

1313

CDS

 

Glyma12g29720

Auxin response factor

I

25

1626

CDS

gma-miR162

Glyma12g35400*

embryo-related protein

IV

13

995

CDS

 

Glyma13g35110*

embryo-related protein

IV

13

963

CDS

gma-miR164

Glyma17g10970#

NAC family transcription factor

I

750

795

CDS

 

Glyma05g00930#

NAC family transcription factor

II

750

751

CDS

 

Glyma06g21020#

NAC family transcription factor

I

750

741

CDS

 

Glyma04g33270#

NAC family transcription factor

I

750

634

CDS

 

Glyma13g34950*

NAC family transcription factor

I

153

747

CDS

 

Glyma12g35530*

NAC family transcription factor

II

153

712

CDS

 

Glyma15g40510#

NAC family transcription factor

II

34

730

CDS

 

Glyma08g18470#

NAC family transcription factor

II

34

731

CDS

 

Glyma12g26190

NAC family transcription factor

I

87

778

CDS

miRNA

Target gene

Target annotation

Class

Abundance(TP10M)

cleavage site(nt)

target site location

gma-miR164

Glyma06g35660

NAC family transcription factor

I

24

811

CDS

gma-miR166

Glyma15g13640#b

HD-ZIP transcription factor

II

273

568/570

CDS

 

Glyma08g21610#b

HD-ZIP transcription factor

II

235

898

CDS

 

Glyma04g09000#

HD-ZIP transcription factor

II

273

93-95

CDS

 

Glyma07g01950#

HD-ZIP transcription factor

II

273

618/620

CDS

 

Glyma08g21620#

HD-ZIP transcription factor

II

273

789/791

CDS

 

Glyma07g01940#

HD-ZIP transcription factor

II

273

919/921

CDS

 

Glyma06g09100#b

HD-ZIP transcription factor

II

273

567/569

CDS

 

Glyma05g30000*

HD-ZIP transcription factor

II

59

1041

CDS

 

Glyma08g13110*

HD-ZIP transcription factor

II

59

571

CDS

 

Glyma09g02750*

HD-ZIP transcription factor

II

59

568

CDS

 

Glyma12g08080#

HD-ZIP transcription factor

II

160

1239

CDS

 

Glyma11g20520#

HD-ZIP transcription factor

II

160

605/607

CDS

gma-miR167

Glyma15g09750*

Auxin response factor

II

159

2444

CDS

 

Glyma13g29320*

Auxin response factor

II

159

3359

CDS

 

Glyma05g27580#

Auxin response factor

II

86

2288

CDS

 

Glyma08g10550#

Auxin response factor

II

86

2477

CDS

 

Glyma18g05330

Auxin response factor

II

54

2880

CDS

 

Glyma15g00770

zinc finger family protein

I

112

1815

5'UTR

 

Glyma02g40650

Auxin response factor

II

76

2924

CDS

gma-miR168

Glyma16g34300#

AGO protein

II

74

534

CDS

 

Glyma09g29720#

AGO protein

II

74

409

CDS

gma-miR169

Glyma08g45030*

NUCLEAR FACTORY

II

31

1294

5'UTR

 

Glyma18g07890*

NUCLEAR FACTORY

I

31

957

CDS

 

Glyma17g05920#

NUCLEAR FACTORY

I

64

1262

5'UTR

 

Glyma13g16770#

NUCLEAR FACTORY

II

64

1022

CDS

 

Glyma09g07960*

NUCLEAR FACTORY

II

33

931

5'UTR

 

Glyma15g18970*

NUCLEAR FACTORY

II

33

981

5'UTR

 

Glyma19g38800

NUCLEAR FACTORY

I

23

1385

5'UTR

gma-miR171

Glyma08g08590#

polyubiquitin protein

IV

13

195

CDS

 

Glyma05g25610#

polyubiquitin protein

IV

13

187

CDS

 

Glyma09g04950

TCP family transcription factor

IV

19

39

3'UTR

gma-miR172

Glyma19g35560*

heat shock cognate protein

IV

47

282

CDS

 

Glyma03g32850*

heat shock cognate protein

IV

47

480

CDS

 

Glyma15g04930#

AP2 transcription factor

II

425

1279

CDS

 

Glyma13g40470#

AP2 transcription factor

II

348

1798

CDS

 

Glyma11g15650#

AP2 transcription factor

II

425

1811

5'UTR

 

Glyma12g07800#

AP2 transcription factor

II

425

1763

CDS

 

Glyma01g39520*

AP2 transcription factor

II

44

1709

CDS

 

Glyma11g05720*

AP2 transcription factor

II

44

1777

CDS

 

Glyma19g36200#

AP2 transcription factor

II

111

1447

CDS

 

Glyma03g33470#

AP2 transcription factor

II

111

1243

CDS

miRNA

Target gene

Target annotation

Class

Abundance(TP10M)

cleavage site(nt)

target site location

gma-miR172

Glyma17g18640

AP2 transcription factor

III

26

1973

CDS

 

Glyma02g09600

AP2 transcription factor

II

78

1469

CDS

 

Glyma05g27370#

TCP family transcription factor

II

109

922

5'UTR

gma-miR319

Glyma13g29160#

TCP family transcription factor

II

112

2078

CDS

 

Glyma08g10350#

TCP family transcription factor

II

109

1172

CDS

 

Glyma15g09910#

TCP family transcription factor

II

112

959

CDS

 

Glyma13g34690*

TCP family transcription factor

II

195

656

CDS

 

Glyma12g35720*

TCP family transcription factor

II

195

1223

CDS

 

Glyma14g06680#

Plasma membrane intrinsic protein

III

49

935

CDS

 

Glyma02g42220#

Plasma membrane intrinsic protein

III

49

1029

5'UTR

 

Glyma13g36840*

TCP family transcription factor

II

73

1220

CDS

 

Glyma12g33640*

TCP family transcription factor

II

73

740

CDS

gma-miR390

Glyma15g14670

expressed protein

IV

14

569

CDS

gma-miR393

Glyma03g36770#

Auxin signaling F-BOX protein

II

65

1750

CDS

 

Glyma19g39420#

Auxin signaling F-BOX protein

II

65

1751

CDS

 

Glyma16g05500*

Auxin signaling F-BOX protein

II

46

2279

CDS

 

Glyma19g27280*

Auxin signaling F-BOX protein

II

46

2207

CDS

 

Glyma10g02630#

Auxin signaling F-BOX protein

IV

14

2166

CDS

 

Glyma02g17170#

Auxin signaling F-BOX protein

IV

14

1741

CDS

gma-miR394

Glyma01g06230*

NADP+

IV

24

42

CDS

 

Glyma06g01850*

NADP+

IV

24

588

CDS

gma-miR396

Glyma03g02500#

Growth regulating factor

I

57

550

CDS

 

Glyma01g34650#

Growth regulating factor

I

57

128

CDS

 

Glyma09g34560*

Growth regulating factor

I

361

323

CDS

 

Glyma01g35140*

Growth regulating factor

II

361

290

CDS

 

Glyma07g04290#

Growth regulating factor

II

117

473

CDS

 

Glyma16g00970#

Growth regulating factor

I

117

353

CDS

 

Glyma13g16920*

Growth regulating factor

I

77

742

CDS

 

Glyma17g05800*

Growth regulating factor

I

77

422

CDS

 

Glyma09g07990*

Growth regulating factor

II

77

380

CDS

 

Glyma11g11820#

Growth regulating factor

I

279

386

CDS

 

Glyma11g01060#

Growth regulating factor

II

279

349

CDS

 

Glyma12g01730#

Growth regulating factor

II

279

504

CDS

 

Glyma01g44470#

Growth regulating factor

I

279

428

CDS

 

Glyma17g35090*

Growth regulating factor

II

1007

913

CDS

 

Glyma17g35100*

Growth regulating factor

II

1007

724

CDS

 

Glyma14g10090*

Growth regulating factor

II

1007

704

CDS

 

Glyma04g40880

Growth regulating factor

I

46

233

CDS

 

Glyma06g13960

Growth regulating factor

II

46

831

CDS

 

Glyma13g22840

Growth regulating factor

IV

13

282

3'UTR

 

Glyma14g10100

Growth regulating factor

II

373

711

CDS

 

Glyma15g19460

Growth regulating factor

II

69

347

CDS

miRNA

Target gene

Target annotation

Class

Abundance(TP10M)

cleavage site(nt)

target site location

gma-miR398

Glyma15g13870

MtN19-like protein

I

15

172

CDS

 

Glyma14g39910

Serine-type endopeptidase

II

87

1370

CDS

 

Glyma19g42890

Copper/zinc superoxide dismutase

III

30

174

CDS

gma-miR1509a

Glyma05g24110

elongation factor

IV

15

436

CDS

gma-miR1511a

Glyma10g05580*

60S ribosomal protein

II

28

1220

CDS

 

Glyma13g19930*

60S ribosomal protein

III

28

1318

CDS

gma-miR1514a

Glyma11g35820#

NSF attachment protein

IV

13

651

CDS

 

Glyma18g02590#

NSF attachment protein

IV

13

615

CDS

 

Glyma07g05370

NAC family transcription factor

II

19

832

CDS

 

Glyma16g01940

NAC family transcription factor

II

25

844

CDS

 

Glyma16g01930

NAC family transcription factor

I

47

742

CDS

gma-miR1515a

Glyma12g00830

Autophagy protein

III

17

889

CDS

gma-miR1516a

Glyma04g42690

Disulfide isomerase

III

33

1016

CDS

gma-miR1522a

Glyma03g36390

FAD linked oxidase family protein

III

45

1826

5'UTR

gma-miR1523a

Glyma20g27950

polyubiquitinated protein

IV

114

864

CDS

gma-miR1530a

Glyma10g32330#

Auxin inducible transcription factor

III

24

79

3'UTR

 

Glyma20g35280#

Auxin inducible transcription factor

III

24

445

CDS

 

Glyma09g41100

expressed protein

II

20

1324

5'UTR

 

Glyma02g28890

transketolase

III

104

67

CDS

gma-miR1536a

Glyma19g06340#

ribulose-1,5-bisphosphate carboxylase

III

108

795

5'UTR

 

Glyma19g06370#

ribulose-1,5-bisphosphate carboxylase

III

108

668

5'UTR

 

Glyma13g07610

ribulose-1,5-bisphosphate carboxylase

III

115

661

5'UTR

  1. CDS: coding sequence; UTR: untranslated region; TP10M: transcripts per 10 million; Cleavage site: nucleotide number from 5' end of cDNA; Adjacent target genes with same # or * were matched by identical reads; alegume or soybean specific miRNAs; bMiRNA targets validated by RLM-5' RACE.
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BMC Plant Biology

ISSN: 1471-2229

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