Table 3 Target prediction of the miRNAs differentially expressed in A. thaliana callus tissues in response to LPS elicitation

miR156

AT5G43270.1

TGACAGAAGAGAGTGAGCAC

GUGCUCUCUCUCUUCUGUCA

1.0

1188

1207

Squamosa promoter binding protein-like 2

miR158

AT1G64100.1

TCCCAAATGTAGACAAAGCA

UUCUUUGUCUACAUUUGGCA

2.5

477

496

Pentatricopeptide (PPR) repeat-containing

miR159

AT2G32460.1

TTTGGATTGAAGGGAGCTCTA

UAGAGCUUCCUUCAAACCAAA

2.0

1004

1024

Myb domain protein 101, ACC synthase

miR160

AT2G28350.1

TGCCTGGCTCCCTGTATGCCA

GGAAUACAGGGAGCCAGGCA

1.0

1330

1349

Auxin response factor 10

miR162

AT1G01040.1

TCGATAAACCTCTGCATCCAG

CUGGAUGCAGAGGUAUUAUCGA

2.0

3422

3443

DICER-LIKE1

miR165

AT2G34710.1

TCGGACCAGGCTTCATCCCCC

UGGGAUGAAGCCUGGUCCGG

1.5

871

890

Homeobox-leucine zipper family protein

miR166

AT2G34710.1

TTCGGACCAGGCTTCATTCCCC

GGGAUGAAGCCUGGUCCGGA

1.0

872

891

Homeobox-leucine zipper family

miR167

AT1G67120.1

GATCATGTTCGCAGTTTCACC

GGUGAAACUGCGUCACAUGAUC

3.0

1909

1930

Transcription factor binding; ARF6

mIR169

AT1G17590.1

TAGCCAAGGATGACTTGCCT

AGGGAAGUCAUCCUUGGCUG

1.5

1233

1252

CCAAT-binding TF (CBF-B/NF-YA)

miR2934

AT1G49770.1

TCTTTCTGCAAACGCCTTGGA

CCAAGGCUUAUGCAGAGAGA

2.5

992

1011

bHLH DNA-binding superfamily protein

miR319

AT3G15030.1

TTGGACTGAAGGGAGCTCCTTC

GAGGGGUCCCCUUCAGUCCAG

2.5

1476

1496

TCP family transcription factor 4

miR396

AT2G36400.1

TTCCACAGCTTTCTTGAACTG

CCGUUCAAGAAAGCCUGUGGAA

2.0

746

767

Growth-regulating factor 4

miR398

AT4G27050.2

GGGTTGATATGAGAACACACG

GUGUGUUUUUAUGUCAAUCU

2.5

154

173

F-box/RNI-like superfamily protein

miR399

AT2G33770.1

TGCCAAAGGAGAGTTGCCCTG

AGGGCAAAUCUUCUUUGGCA

1.5

608

627

Ubiquitin-protein ligase

miR401

AT5G34863.1

ACAATGGAGATTAGGAGACATTTT

AAAAUGUCUCCUUAUCUCCAUUGU

1.0

329

352

Transposable element gene

miR403

AT1G31280.1

GGATTAGATTCACGCACAAACTC

GAGUUUGUGCGUGAAUCUAAUUG

1.5

3223

3245

AGO2 | Argonaute family protein

miR405

AT1G27880.1

AAATGAGTTATGGGTTAGACCCGT

GUCUGGUCCAAGACUCAUUU

3.0

2633

2653

DEAD/DEAH box RNA helicase family protein

miR407

AT3G20220.1

GGGGAAAAATGTCAAAAAAATCGC

UGAUUUUUUUGAUAUCUUUCUUU

3.0

197

219

SAUR-like auxin-responsive protein family

miR408

AT2G02850.1

TGCACTGCCTCTTCCCTGGCT

CCAAGGGAAGAGGCAGUGCA

2.0

97

116

Plantacyanin

miR5026

AT3G62340.1

AAAGTTAGTAACTCAAAGGCTCGT

AGCUUUUGAGUUUUUAACUUC

3.0

166

186

WRKY68, AtWRKY68 | WRKY family TF

miR5029

AT4G04570.1

AAUGAGAGAGAACACUGCAAA

UUGUGGUGUUUACUUUCAUU

3.0

964

983

Cysteine-rich RLK

miR5635

AT1G20230.1

ATTTAATACCTGAACTTTCAAAGA

UGGAAAGUUCAGGUAUUGAGG

3.0

623

643

Pentatricopeptide repeat (PPR)

miR5638

TCCACACTAGTGTAACGACAGTG

Unknown

miR5641

AT3G43571.1

CATGGAGGAGATATTTGGTAA

UUAUCUAAUAUUUCUUCCAUG

2.5

528

548

Transposable element gene

miR5642

AT5G04010.1

CAAGAACATCTTCGTTACGGAT

AGUUUUAAUGAAGAUGUUCUUG

2.5

754

775

F-box family protein

miR5643

AT1G71840.1

AGAAGACACAGAGACAAAGACTCA

GGGUUUUUGUACUUUGUGUCUUCU

3.0

71

94

Transducin WD-40 repeat family protein

miR5651

AT1G43260.1

TCGTTACTATTTGAACCGCACC

UGUUGUUCAAGUAGUAACGA

2.0

504

523

hAT transposon superfamily protein

miR5655

AT5G02480.1

CTTTTCCTCCTCCTCCACCACC

GGUGGUGGAGGAGGAGGAGGAG

1.0

992

1013

HSP20-like chaperones superfamily protein

miR5662

AT5G60410.1

AGAGGAAAATATAGAGATCACCAT

UGGUUGUCUUUUUAUUUUCCUCU

3.0

10

32

DNA-binding protein: MIZ/SP-RING Zinc finger, PHD-finger

miR773

AT5G64270.1

TTTGCTTCCAGCTTTTGTC

AGACGGAAGAUGGAAGCAGA

172

191

Splicing factor, putative

miR782

AT3G29152.1

TCTTTCTGCAAACGCCT

AGAACACCAAACGUGUUUGU

260

279

Protease inhibitor/seed storage/LTP family protein

miR783

AT5G43530.1

CAAAAGATCTGGTGATGAAGTTGA

UGGACUUCAUUUUUGGAUCUUUUG

3.0

3406

3429

Helicase protein with RING/U-box domain

miR822

AT5G02330.1

GCGGGAAGCATTTGCACATGTT

AGCAUGUGCAAAUGCUUCUCGC

0.5

1254

1275

Cysteine/Histidine-rich C1 domain family protein

miR824

AT3G08870.1

CCTTCTCATCGATGGTCTAGA

UUUAGGCCAUCGAUGAGAAUG

2.5

1873

1893

Concanavalin A-like lectin protein kinase protein

miR829

AT5G18560.1

AGCTCTGATACCAAATGA

UUACCUUGAAGUUUUGAUUUG

1.5

1284

1304

AP2 domain-containing TF/ ethylene response factor

mIR842

AT1G60130.1

CATGGTCAGATCCGTCATCCC

GGGAUGAUGGAUCCGACCAUG

1.5

86

106

Mannose-binding lectin superfamily protein

miR855

AT5G02490.1

AAACTCGAAAGCGTCTAGGACTTT

ACUUUUUCUUAGCUUUUUCU

3

47

66

Heat shock cognate 70 kDa protein 2 (HSC70-2) (HSP70-2)