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Table 3 Targets of P. trichocarpa miRNAs verified by degradome sequencing

From: Identification of drought-responsive and novel Populus trichocarpamicroRNAs by high-throughput sequencing and their targets using degradome analysis

miRNA

Target transcript

Category

Cleavage

Reads at

Position

Target annotation

   

Site

Cleavage

Penalty

 
    

Site

Score

 

Ptc-miR156k

POPTR_0013s06910.1

III

799

224

4

Glucose-6-phosphate/phosphate

Ptc-miR159a-c

POPTR_0011s11490.1

III

428

153

4

Methionine sulfoxide reductase B 1

Ptc-miR159e

POPTR_0006s16050.1

III

1014

134

4

Catalytic

Ptc-miR159f

POPTR_0002s05060.1

III

372

99

4

Protein kinase

Ptc-miR164f

POPTR_0007s12070.1

III

623

337

4

PS II oxygen-evolving complex 1

Ptc-miR164f

POPTR_0005s13860.1

III

623

337

4

PS II oxygen-evolving complex 1

Ptc-miR166a-q

POPTR_0009s01990.1/2

I

574

469

3

Transcription factor

Ptc-miR166a-q

POPTR_0004s22090.1

I

563

766

2.5

Transcription factor

Ptc-miR167a-e

POPTR_0012s09730.1

I

946

694

3.5

NOP56 (Arabidopsis homolog of

      

nucleolar protein)

Ptc-miR167f/g

POPTR_0013s01580.1

II

285

239

4

Function unknown

Ptc-miR169z

POPTR_0018s11310.1

III

2204

118

4

Eukaryotic translation initiation factor 4F

Ptc-miR171l-n

POPTR_0003s06200.1

III

1615

89

3

Function unknown

Ptc-miR172a-c/f

POPTR_0014s06330.1

III

799

110

4

Glycoprotease M22 family

Ptc-miR172d/e

POPTR_0016s02570.1

III

103/172

1222

4

Function unknown

Ptc-miR172d/e

POPTR_0001s44680.1

III

186

111

4

Apolipoprotein D-related

Ptc-miR172g/h

POPTR_0001s44680.1

III

186

111

3.5

Apolipoprotein D-related

Ptc-miR172i

POPTR_0015s13920.1

III

446

174

3.5

Chlororespiration reduction 1

Ptc-miR390a-d

POPTR_0017s07350.1

II

2472

689

3.5

LOX2 (lipoxygenase 2)

Ptc-miR390a-d

POPTR_0001s05330.1

II

2622

689

3.5

LOX2 (lipoxygenase 2)

Ptc-miR390a-d

POPTR_0005s11640.1

III

9458

108

4

FAT domain-containing protein

Ptc-miR390a-d

POPTR_0328s00200.1

II

2622

1180

3.5

LOX2 (lipoxygenase 2)

Ptc-miR396a/b

POPTR_0004s18020.1/2

III

547

140

3.5

MYB4

Ptc-miR396f

POPTR_0004s18020.1/2

III

547

140

3.5

MYB4

Ptc-miR397c

POPTR_0002s01740.1

III

135

163

3.5

PETE1 (plastocyanin 1)

Ptc-miR397c

POPTR_0009s05960.1

III

1660

104

4

Hydrolase

Ptc-miR398a

POPTR_0010s06990.1/2

III

1428

346

4

DC1 domain-containing

Ptc-miR473a

POPTR_0602s00210.1

I

850

327

4

VEP1 (vein patterning 1)

Ptc-miR475d

POPTR_0003s20310.1/3

I

1898

544

4

Zinc finger (CCCH-type) family protein

Ptc-miR476a

POPTR_0001s21140.1

III

145

137

3.5

Post-illumination chlorophyll

      

Fluorescence increase protein

Ptc-miR403a-c

POPTR_0016s03150.1

III

637

156

4

Cytochrome p450

Ptc-miR403a-c

POPTR_0016s03160.1

III

634

156

4

Cytochrome p450

Ptc-miR482.1

POPTR_0017s06100.1

I

1247

1312

3.5

UDP-glucosyl transferase

Ptc-miR482.1

POPTR_0009s13280.1

III

1036

94

4

Translation initiation factor

Ptc-miR482.1

POPTR_0010s13860.1

III

152

101

4

ATP-dependent Clp protease

      

Adaptor protein

Ptc-miR482.1

POPTR_0017s06080.1

I

914

1312

3.5

UDP-glucosyl transferase

Ptc-miR482.1

POPTR_0322s00200.1

I

1247

1312

3.5

UDP-glucosyl transferase

Ptc-miR482.1

POPTR_0017s06120.1

I

1010

1312

3.5

UDP-glucosyl transferase

Ptc-miR482.1

POPTR_0001s27260.1

III

1033

144

3.5

Carotenoid cleavage dioxygenase 1

Ptc-miR482.1

POPTR_0009s06530.1

III

1051

144

4

Carotenoid cleavage dioxygenase 1

Ptc-miR482.1

POPTR_0007s00550.1

III

337

228

4

NADP-dependent

Ptc-miR530b

POPTR_0002s24070.1

III

424

104

4

Photosystem I subunit L

Ptc-miR1444a

POPTR_0014s10790.1

III

2569

159

3.5

Preprotein translocase secA

Ptc-miR1444a

POPTR_0014s11380.1

III

2368

135

3.5

Pentatricopeptide (PPR)

Ptc-miR1446a-e

POPTR_0014s06190.1/2

II

677

511

4

Unfertilized embryo sac 10

Ptc-miR1446a-e

POPTR_0001s34380.1/2

III

295

178

4

16S rRNA processing

Ptc-miR1446a-e

POPTR_0011s13770.2

III

55

204

3.5

UBQ10 (Polyubiquitin 10)

Ptc-miRn6

POPTR_0001s11990.1/2/3

III

259

98

1

Function unknown

Ptc-miRn7

POPTR_0001s11990.1/2/3

III

259

98

0.5

Function unknown

Ptc-miRn7

POPTR_0014s01740.1/2

II

723

366

3.5

APT1 (Adenine phosphoribosyl

      

transferase 1)

Ptc-miRn8

POPTR_0001s40480.1

III

656

1443

4

Glycolate oxidase

Ptc-miRn13

POPTR_0018s08940.1

III

1605

116

4

Abnormal inflorescence meristem

Ptc-miRn26

POPTR_0016s00510.1

III

1233

265

4

Heat shock protein 81-4

Ptc-miRn30

POPTR_0002s07540.1

III

528

75

3.5

SKP2A (F-box protein)

Ptc-miRn32

POPTR_0014s16800.1

III

504

93

4

Beta-catenin repeat family protein

Ptc-miRn33

POPTR_0019s08960.1

III

3244

134

4

Function unknown

Ptc-miRn37

POPTR_0003s08800.1

III

585

108

4

Pentatricopeptide (PPR)

Ptc-miRn38

POPTR_0011s17280.1

III

584

170

4

PEX5 (Peroxin 5)

      

Signal-1 binding

Ptc-miRn40

POPTR_0001s07220.1

III

305

79

2

mTERF(mitochondrial transcription

      

termination factor family protein)

Ptc-miRn40

POPTR_0005s20140.1

III

1030

119

4

Thylakoidal ascorbate peroxidase

Ptc-miRn49

POPTR_0011s01280.1

III

791

90

4

Copper/zinc-superoxide

      

dismutase 2

  1. ‘Cleavage site’, the cleavage site location at the area of coding sequence; ‘Position penalty score’, the same penalty score as the prediction of new miRNA targets; ‘MFE’, minimum free energy of the stem loop structure. The bold font of transcripts indicates that they were identified by prediction.