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Table 2 Targets for known miRNA in peach identified by degradome sequencing

From: Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

miRNA

Target genea

Align scoreb

Normalized reads at cleavage site (tpb)c

Categoryd

Target gene annotation

Conserved targets for conserved miRNAs

miR156

ppa006611m

3

150.2

3

Squamosa promoter-binding-like protein

miR156

ppa007056m

2

500.7

2

Squamosa promoter-binding-like protein

miR156

ppa021582m

2

1151.5

2

Squamosa promoter-binding-like protein

miR156

ppa024285m

3

3704.8

0

Squamosa promoter-binding-like protein

miR159

ppa003628m

3.5

2252.9

0

MYB transcription factor

miR160

ppa002082m

1

1301.7

2

Auxin response factor

miR160

ppa002710m

1

1251.6

2

Auxin response factor

miR164

ppa007653m

2.5

11214.7

0

NAC domain-containing protein

miR165

ppa001343m

2.5

2353.1

2

Homeobox-leucine zipper protein

miR165

ppa001378m

2.5

4856.3

0

Homeobox-leucine zipper protein

miR166

ppa001343m

3

2353.1

2

Homeobox-leucine zipper protein

miR166

ppa001378m

3

4856.3

0

Homeobox-leucine zipper protein

miR167

ppa001179m

4.5

1201.6

2

Auxin response factor

miR168

ppa000619m

4

275.4

2

Argonaute protein

miR168

ppa000900m

4

275.4

2

Argonaute protein

miR169

ppa006634m

3.5

1226.6

2

Nuclear transcription factor Y subunit A

miR390

AJ875750 (EST)

   

PpTAS3

miR393

ppa003344m

1

1401.8

2

Auxin signaling F-box protein

miR393

ppa003465m

2

550.7

3

Auxin signaling F-box protein

miR395

ppa002425m

2

600.8

2

Sulfate transmembrane transporter

miR396

ppa003017m

3.5

4005.2

0

Growth-regulating factor

miR396

ppa006912m

3

4956.5

2

Growth-regulating factor

miR396

ppa011917m

3.5

7960.4

0

Growth-regulating factor

miR396

ppa019623m

3

9312.2

0

Growth-regulating factor

miR396

ppa021277m

4

22179.0

0

Growth-regulating factor

miR396

ppa022199m

3

28086.7

0

Growth-regulating factor

miR396

ppa024293m

3

700.9

2

Growth-regulating factor

miR397

ppa003308m

4

550.7

2

Laccase

miR397

ppa003408m

3

300.4

3

Laccase

miR397

ppa003646m

1.5

9011.8

0

Laccase

miR397

ppa003714m

3

400.5

3

Laccase

miR397

ppa022440m

1.5

250.3

3

Laccase

miR408

ppa018507m

1

1051.4

2

Copper ion binding protein

miR408

ppa021383m

3

3104.1

2

Copper ion binding protein

Tas3-siRNA

ppa001557m

2

650.9

2

Auxin response factor

Tas3-siRNA

ppa001392m

1.5

22529.4

2

Auxin response factor

Novel targets for conserved miRNAs

     

miR396

ppa003643m

4

400.5

3

Rho guanyl-nucleotide exchange factor

miR408

ppa004802m

3.5

500.7

3

Selenium-binding protein

miR408

ppa007350m

4

3404.4

2

Cyclin D3

Targets for other known miRNAs

     

miR505

ppa012208m

4.5

275.4

2

ATP synthase

miR505

ppa012241m

4.5

275.4

2

ATP synthase

miR530

ppa004922m

4

50.1

4

ATP binding

miR828

ppa010908m

1

55247.2

0

MYB transcription factor

miR828

ppa016135m

3

2152.8

2

MYB transcription factor

miR828

ppa024533m

2

1852.4

2

MYB transcription factor

miR858

ppa005421m

4.5

851.1

2

3-ketoacyl-CoA thiolase

miR858

ppa006057m

4.5

851.1

2

3-ketoacyl-CoA thiolase

miR858

ppa006769m

4

150.2

3

MYB transcription factor

miR858

ppa009143m

4

150.2

3

MYB transcription factor

miR858

ppa010252m

4

3754.9

2

MYB transcription factor

miR858

ppa015883m

3

650.9

0

MYB transcription factor

miR858

ppa016135m

3.5

16481.5

2

MYB transcription factor

miR858

ppa016385m

4

1201.6

0

MYB transcription factor

miR858

ppa016708m

4.5

650.9

2

MYB transcription factor

miR858

ppa017136m

3.5

35.0

3

MYB transcription factor

miR858

ppa018561m

4

1201.6

2

MYB transcription factor

miR858

ppa019380m

4

35.0

1

MYB transcription factor

miR858

ppa022205m

4

4070.3

0

MYB transcription factor

miR858

ppa022431m

4.5

6959.1

2

MYB transcription factor

miR858

ppa022465m

3.5

16481.5

0

MYB transcription factor

miR858

ppa023768m

2.5

3704.8

2

MYB transcription factor

miR858

ppa023812m

3.5

4070.3

0

MYB transcription factor

miR858

ppa024074m

4.5

4070.3

0

MYB transcription factor

miR894

ppa005211m

4

300.4

3

Ankyrin repeat family protein

miR2478

ppa024560m

4.5

300.4

3

Disease resistance-responsive protein

miR2911

ppa004713m

4.5

2052.7

2

Vacuolar processing enzyme

miR2916

ppa008099m

4.5

200.3

2

Galacturonosyltransferase-like protein

miR4171-5

ppa010474m

4.5

650.9

2

C3HC4-type RING finger family protein

miR4171-5

ppa012554m

4

150.2

3

Universal stress protein (USP)

  1. a Target gene is the identified transcript from the peach transcriptome (http://www.rosaceae.org/node/35) or the EST sequence in the case of miR390.
  2. b Align score is calculated according to [7].
  3. c tpb, transcripts per billion, according to [21].
  4. d Category 0: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript; Category 1: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; Category 2: >1 raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; Category 3: >1 raw read at the position, abundance at position is equal to or less than the median for the transcript; Category 4: Only 1 raw read at the position.