Table 3 Potential targets of the identified known miRNAs from Malus hupehensis leaves by degradome analysis

mdm-miR156

Squamosa promoter-binding protein-like

transcription factor

AT1G69170.1

MDP0000119458 ;MDP0000778465;MDP0000589558

(SBP domain) transcription factor family protein

MDP0000142582; MDP0000146640; MDP0000171877

MDP0000176265 ;MDP0000193702; MDP0000210138

MDP0000246046 ;MDP0000263766

mdm-miR156

squamosa promoter binding protein-like 2(SPL2)

transcription factor

AT5G43270.1

MDP0000155354

mdm-miR156

squamosa promoter binding protein-like 9(SPL9)

transcription factor

AT2G42200.1

MDP0000297978;MDP0000322647

mdm-miR156

acyl-CoA synthetase 5

AT1G62940.1

MDP0000249364

mdm-miR159

myb domain protein 65

transcription factor

AT3G11440.1

MDP0000147309

mdm-miR160

auxin response factor 16

transcription factor

AT4G30080.1

MDP0000131481; MDP0000221322; MDP0000750392

mdm-miR160

auxin response factor 17

transcription factor

AT1G77850.1

MDP0000232116; MDP0000256621

mdm-miR160

Co-chaperone GrpE family protein

AT1G36390.1

MDP0000273491

mdm-miR162

LETM1-LIKE protein

AT3G11560.2

MDP0000187512

mdm-miR164

NAC domain containing protein 1

AT1G56010.2

MDP0000298182; MDP0000528658

mdm-miR166

homeobox gene 8

AT4G32880.1

MDP0000005879; MDP0000126553

mdm-miR166

Homeobox-leucine zipper family protein/ lipid-

AT2G34710.1

MDP0000050082;MDP0000943529

binding START domain-containing protein

AT5G60690.1

MDP0000236500; MDP0000242861; MDP0000426630

AT1G52150.3

MDP0000251484

AT1G52150.1

MDP0000313059

mdm-miR167

auxin response factor 6

transcription factor

AT1G30330.2

MDP0000319957; MDP0000550049

AT1G30330.1

MDP0000153538

mdm-miR167

auxin response factor 8

transcription factor

AT5G37020.1

MDP0000137461; MDP0000232417

mdm-miR167

auxin response factor 19

transcription factor

AT1G19220.1

MDP0000268306

mdm-miR168

Stabilizer of iron transporter SufD/ Polynucleotidyl transferase

AT1G48410.1

MDP0000069525; MDP0000161046; MDP0000305971

mdm-miR169

nuclear factor Y, subunit A7

transcription factor

AT1G30500.2

MDP0000164531; MDP0000183865

AT1G30500.1

MDP0000279028

mdm-miR169

nuclear factor Y, subunit A9

transcription factor

AT3G20910.1

MDP0000146933

mdm-miR169

translocation protein-related

AT5G12840.1

MDP0000296077

mdm-miR171

GRAS family transcription factor

transcription factor

AT4G00150.1

MDP0000151144 ;MDP0000275704 ;MDP0000274120

AT2G45160.1

MDP0000784909

mdm-miR172

related to AP2.7

transcription factor

AT2G28550.3

MDP0000163645; MDP0000181606; MDP0000200319;

MDP0000296716

mdm-miR172

Integrase-type DNA-binding superfamily protein

transcription factor

AT4G36920.1

MDP0000137561

mdm-miR319

myb domain protein 65

transcription factor

AT3G11440.1

MDP0000147309

mdm-miR3627

AT hook motif DNA-binding family protein

AT2G45850.1

MDP0000133746;MDP0000231744

mdm-miR3627

autoinhibited Ca2+ − ATPase, isoform 8

AT5G57110.1

MDP0000258197

mdm-miR390

exocyst subunit exo70 family protein H7

AT5G59730.1

MDP0000145463

mdm-miR391

Transmembrane proteins 14C

AT3G43520.1

MDP0000207199; MDP0000244081

mdm-miR393

F-box/RNI-like superfamily protein

AT3G62980.1

MDP0000125975; MDP0000498419

mdm-miR393

auxin signaling F-box 2

AT3G26810.1

MDP0000203334; MDP0000469943

mdm-miR393

auxin signaling F-box 3

AT1G12820.1

MDP0000268652

mdm-miR395

ATP sulfurylase 1

AT3G22890.1

MDP0000263161

mdm-miR398

DC1 domain-containing protein

AT1G60420.1

MDP0000152817 ;MDP0000308890

mdm-miR398

GroES-like zinc-binding dehydrogenase family protein

AT5G43940.1

MDP0000193167

mdm-miR5225

autoinhibited Ca2+ − ATPase, isoform 8

AT5G57110.1

MDP0000258197

mdm-miR535

Papain family cysteine protease(RD19)

AT4G39090.1

MDP0000189200

mdm-miR858

myb domain protein 3

transcription factor

AT1G22640.1

MDP0000184538

mdm-miR858

myb domain protein 4

transcription factor

AT4G38620.1

MDP0000031172

mdm-miR858

myb domain protein 5(MYB5)

transcription factor

AT3G13540.1

MDP0000133817; MDP0000143276;

MDP0000226215;MDP0000253904

mdm-miR858

myb domain protein 7

transcription factor

AT2G16720.1

MDP0000210851

mdm-miR858

myb domain protein 12

transcription factor

AT2G47460.1

MDP0000140609 ;MDP0000887107

mdm-miR858

myb domain protein 66

AT5G14750.1

MDP0000124555

mdm-miR858

Duplicated homeodomain-like superfamily protein

AT5G35550.1

MDP0000318013; MDP0000437717

mdm-miR858

high response to osmotic stress 10

AT1G35515.1

MDP0000931057