Table 4 Potential targets of the identified novel miRNAs from Malus hupehensis leaves by degradome analysis

novel_mir_106

Late embryogenesis abundant (LEA) hydroxyproline rich glycoprotein family

AT2G46150.1

MDP0000405151

novel_mir_108

RNA-binding (RRM/RBD/RNP motifs) family protein

AT2G44710.1

MDP0000242219;MDP0000303270

novel_mir_11

Flavin-containing monooxygenase family protein

AT1G48910.1

MDP0000138851;MDP0000208234

novel_mir_157

myb domain protein 105

transcription factor

AT1G69560.1

MDP0000136541; MDP0000146675

novel_mir_116

autoinhibited Ca2+ − ATPase, isoform 8

AT5G57110.1

MDP0000258197

novel_mir_156

phosphate transporter 1;4

AT2G38940.1

MDP0000141330; MDP0000523104

novel_mir_156

phosphate transporter 1;7

AT3G54700.1

MDP0000746621

novel_mir_160

Transmembrane proteins 14C

AT3G43520.1

MDP0000207199; MDP0000244081

novel_mir_169

RING/U-box superfamily protein

AT3G05200.1

MDP0000909888

novel_mir_169

Integrase-type DNA-binding superfamily protein

AT3G23230.1

MDP0000930655

novel_mir_207

phytosulfokine 4 precursor

AT3G49780.1

MDP0000145144 ;MDP0000509438; MDP0000824044

novel_mir_261

cell elongation protein / dwarf1 / diminuto (dim)

AT3G19820.1

MDP0000278275; MDP0000682675

novel_mir_262

nuclear factor Y, subunit A9

transcription factor

AT3G20910.1

MDP0000146933

novel_mir_262

nuclear factor Y, subunit A7

transcription factor

AT1G30500.2

MDP0000164531 ;MDP0000183865

AT1G30500.1

MDP0000279028

novel_mir_262

nuclear factor Y, subunit A1

transcription factor

AT5G12840.1

MDP0000296077

novel_mir_268

nuclear factor Y, subunit A7

transcription factor

AT1G30500.2

MDP0000164531 ;MDP0000183865

AT1G30500.1

MDP0000279028

novel_mir_27

plasmodesmata-located protein 2

AT1G04520.1

MDP0000412849

novel_mir_301

phospholipid/glycerol acyltransferase family protein

AT1G32200.1

MDP0000171689 ;MDP0000532750

novel_mir_335

SOS3-interacting protein 4

AT2G30360.1

MDP0000127732; MDP0000146449

novel_mir_351

response regulator 2

AT4G16110.1

MDP0000228719

novel_mir_37

Translation initiation factor IF6

AT3G55620.1

MDP0000247249

novel_mir_374

S-adenosyl-l-homocysteine (SAH) hydrolase 2

AT3G23810.1

MDP0000212365; MDP0000679173

novel_mir_378

ATP binding; valine-tRNA ligases; nucleotide binding; aminoacyl-tRNA ligases

AT5G16715.1

MDP0000155593; MDP0000238240

novel_mir_384

S-adenosyl-l-homocysteine (SAH) hydrolase 2

AT3G23810.1

MDP0000212365; MDP0000679173

novel_mir_392

nuclear factor Y, subunit A9

transcription factor

AT3G20910.1

MDP0000146933

novel_mir_392

nuclear factor Y, subunit A7

transcription factor

AT1G30500.2

MDP0000164531; MDP0000183865

AT1G30500.1

MDP0000279028

novel_mir_392

nuclear factor Y, subunit A1

transcription factor

AT5G12840.1

MDP0000296077

novel_mir_422

related to AP2 4

transcription factor

AT1G78080.1

MDP0000401140; MDP0000633218

novel_mir_446

S-methyl-5-thioribose kinase

AT1G49820.1

MDP0000148984; MDP0000278395; MDP0000234656

novel_mir_477

aldehyde dehydrogenase 2B4

AT3G48000.1

MDP0000159395; MDP0000221713

novel_mir_477

5\′-3\′ exonuclease family protein

AT1G34380.2

MDP0000259472

novel_mir_477

OPC-8:0 CoA ligase1

AT1G20510.1

MDP0000716496

novel_mir_486

phospholipase D delta

AT4G35790.2

MDP0000125742

novel_mir_486

zinc knuckle (CCHC-type) family protein

AT5G43630.1

MDP0000147872; MDP0000196131

novel_mir_492

BRI1-associated receptor kinase

AT4G33430.1

MDP0000287771; MDP0000291093 ;MDP0000309283

novel_mir_495

ENTH/VHS/GAT family protein

AT1G06210.1

MDP0000320808

novel_mir_506

GDSL-like Lipase/Acylhydrolase superfamily protein

AT3G26430.1

MDP0000182713

novel_mir_89

NB-ARC domain-containing disease resistance protein

AT3G07040.1

MDP0000137113; MDP0000142444 ;MDP0000249156

MDP0000662922; MDP0000242361

novel_mir_89

NB-ARC domain-containing disease resistance protein

AT3G14470.1

MDP0000206335; MDP0000241462 ;MDP0000243301

novel_mir_89

LRR and NB-ARC domains-containing disease resistance protein

AT3G14460.1

MDP0000196621

novel_mir_413

Squamosa promoter-binding protein-like (SBP domain) transcription factor family protein

transcription factor

AT1G69170.1

MDP0000119458; MDP0000146640; MDP0000171877

MDP0000193702; MDP0000246046 ;MDP0000589558

MDP0000778465

AT5G50670.1

MDP0000142582; MDP0000176265; MDP0000210138

MDP0000263766

novel_mir_329

myb domain protein 105

transcription factor

AT1G69560.1

MDP0000146675

novel_mir_329

C2H2-like zinc finger protein

AT1G75710.1

MDP0000179049

novel_mir_329

Frigida-like protein

AT5G27220.1

MDP0000179887

novel_mir_329

RNA-binding protein

AT2G43970.1

MDP0000266270