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Table 2 Example targets for apple miRNAs (or families)a

From: Apple miRNAs and tasiRNAs with novel regulatory networks

miRNA

Target

ASb

RN_readsa (TPB)

Categoryd

Target gene annotation

Conserved targets for conserved miRNAs

miR156

MDP0000146640

1

112.47

0

Squamosa promoter-binding-like protein

miR159

MDP0000147309

4.5

457.13

0

Transcription factor GAMYB

miR164

MDP0000121265

2.5

2,674.73

0

NAC domain-containing protein

miR165/166

MDP0000426630

3

212.24

0

Homeobox-leucine zipper protein

miR167

MDP0000137461

4

62.58

2

Auxin response factor

miR168

MDP0000161046

0

32.65

2

Argonaute protein

miR171

MDP0000151144

2.5

16.33

3

Scarecrow-like protein

miR172

MDP0000281079

3

212.24

0

Ethylene-responsive transcription factor RAP

miR319

MDP0000243495

3

16.33

2

Transcription factor TCP4

miR390

CN490861e

   

MdTAS3

miR393

MDP0000203334

2.5

2.72

3

Auxin signaling F-box protein

miR395

MDP0000121656

3.5

225.84

2

3'-Phosphoadenosine 5'-phosphosulfate synthase

miR396

MDP0000204597

4

32.65

0

Growth regulating factor (GRF)

tasiARFs

MDP0000179650

1

24.49

2

Auxin response factor

Other non-conserved targets for conserved miRNAs

miR319

MDP0000296691

4.5

2.72

4

GDP-mannose 3,5-epimerase

miR396

MDP0000454027

4

5.44

4

IAA-amino acid hydrolase ILR1-like 6

miR399

MDP0000253476

4

21.77

3

Unknown

Targets for other known miRNAs

miR2111

MDP0000416146

4

17.69

2

Unknown

miR3627

MDP0000941000

4

27.21

2

Amino acid transporter

miR535

MDP0000185769

4

27.21

3

Cysteine protease

miR828

MDP0000124555

1

69,205.65

0

MYB transcription factor

miR828

CN490819 (MdTAS4)

2.5

2,065.23

0

Non-coding mRNA

miR858

MDP0000140609

3

1,379.54

0

MYB transcription factor

miR858

MDP0000161125

4.5

351.01

0

Mate efflux family protein

miR858

MDP0000726382

4.5

2.72

3

Lipase family protein

Targets for apple-specific miRNAs

 

miRC3

MDP0000485327

2

326.52

0

Unknown protein

miRC5

MDP0000863013

5

16.33

3

ARO4 (ARMADILLO REPEAT ONLY 4)

miRC6

MDP0000410000

5

16.33

2

Uncharacterized protein

miRC10

MDP0000294365

4

185.03

0

Protein kinase

miRC16

MDP0000737474

5

38.09

2

Uncharacterized protein

miRC25

MDP0000306273

4.5

10.88

2

Cytochrome P450 86B1

miRC29

MDP0000279462

4.5

13.60

2

Oligopeptide transporter 2

miRC42

MDP0000286564

5

27.21

2

Mitogen-activated protein kinase kinase 2

  1. aA detailed list is included in Table S6 in Additional file 1. bThe alignment score (AS) threshold was set to 4.5 and 5 for known and apple-specific miRNAs, respectively. cRN_reads, repeat normalized reads; TPB, transcripts per billion. dCategory 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. eCleavage was predicted based on the distribution of tasiRNAs.
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Genome Biology

ISSN: 1474-760X

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