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Table 2 Identified miRNA targets found in both soybean seed coat and cotyledon

From: Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

miRNA

Tissue

Target

Target Annotation

C.Site

Location

Category

TP100M

P-Value

gma-miR156

C100

Glyma02g13370.1

SBP domain containing protein

1219

CDS

0

92.52237

0.0477

 

C300

Glyma02g13370.1

SBP domain containing protein

1219

CDS

0

27.27151

0.0496

 

SC100

Glyma02g30670.1

SBP domain containing protein

768

CDS

0

335.5574

0.0445

 

C100

Glyma05g00200.1

SBP domain containing protein

1202

CDS

1

57.82648

0.015

gma-miR159*

C25

Glyma04g15150.1

Myb family transcription factor

853

CDS

0

787.7315

0.0111

 

C300

Glyma04g15150.1

MYB family transcription factor

853

CDS

0

178.5044

0.0091

 

C25

Glyma06g47000.1

Myb family transcription factor

852

CDS

0

787.7315

0.0111

 

SC25

Glyma06g47000.1

Myb family transcription factor

852

CDS

0

18.44158

0.0123

 

C300

Glyma06g47000.1

MYB family transcription factor

852

CDS

0

178.5044

0.0091

 

SC100

Glyma13g34710.1

No functional annotation

1161

CDS

2

106.3962

0.0391

 

C300

Glyma13g34710.1

No Functional Annotation

1161

CDS

1

9.916913

0.0133

 

C25

Glyma19g40720.1

Anion Exchange protein

2162

CDS

1

28.27754

0.0157

gma-miR160#

C100

Glyma10g35480.1

Auxin response factor

740

CDS

0

12166.69

0.0168

 

C100

Glyma11g20490.1

Auxin response factor

1510

CDS

0

12166.69

0.0071

 

C100

Glyma12g08110.1

Auxin response factor

1501

CDS

0

12166.69

0.0071

 

C100

Glyma12g29720.1

Auxin response factor

1626

CDS

0

1445.662

0.0168

 

C100

Glyma14g33730.1

Auxin response factor

1184

CDS

0

1144.964

0.027

 

SC25

Glyma04g43350.1

Auxin response factor

1337

CDS

0

1391.022

0.0379

 

C300

Glyma04g43350.1

Auxin response factor

1337

CDS

0

401.635

0.0281

 

SC25

Glyma10g06080.1

Auxin response factor

1355

CDS

0

821.9674

0.0379

gma-miR164*

SC100

Glyma15g40510.1

No apical meristem protein

730

CDS

1

69.56677

0.0013

 

C100

Glyma04g33270.1

No apical meristem protein

634

CDS

0

150.3488

0.0026

 

SC100

Glyma04g33270.1

No apical meristem protein

634

CDS

0

425.585

0.0024

 

SC100

Glyma05g00930.1

No apical meristem protein

751

CDS

2

425.585

0.0433

gma-miR166

SC100

Glyma04g09000.1

START domain containing protein

93

CDS

3

16.36865

0.0478

 

SC100

Glyma05g30000.1

HD-ZIP transcription factor

1041

CDS

3

8.184326

0.0478

 

C25

Glyma05g30000.1

HD-ZIP transcription factor

1041

CDS

0

3389.265

0.0331

 

C300

Glyma05g30000.1

HD-ZIP transcription factor

1041

CDS

0

4321.295

0.0271

gma-miR167*

C100

Glyma15g00770.1

Zinc finger family protein

1815

CDS

0

1480.358

0.0071

 

SC100

Glyma02g18250.3

Elongation Factor S-II

90

CDS

1

3592.919

0.0168

 

C100

Glyma02g40650.1

Auxin response factor

2924

CDS

0

855.8319

0.027

 

SC100

Glyma02g40650.1

Auxin response factor

2924

CDS

0

1239.925

0.0252

 

C25

Glyma02g40650.1

Auxin response factor

2924

CDS

0

2536.899

0.0343

  1. Complete tables can be found in Additional file 1.
  2. CDS: Coding Sequence; UTR: Untranslated Region; TP100M: Transcripts per 100 million; C.site (Cleavage site): Nucleotide number from 5’ end of cDNA; P-value ≤0.05 using Cleaveland pipeline.
  3. Cot25 and SC25 are libraries from cotyledons and seed coats dissected from early-maturation green seed of 25–50 mg fresh wt.; Cot100 and SC100 are cotyledons and seed coats dissected from mid-maturation green seed of 100–200 mg fresh weight range; Cot300 are cotyledons dissected from late maturation yellow seeds of 300–400 mg weight range.
  4. * and bold are miRNAs whose targets shown in the target plots (t-plots) (Figure 1).
  5. # and bold are miRNAs whose RLM-5’RACE validated targets are shown in the target plots (t-plots) (Figure 2).
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BMC Genomics

ISSN: 1471-2164

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