Table 3 Sequence, length, and expression level of differentially expressed wheat miRNAs and C. rosea milRNAs identified during interactions. Values in bold indicate differential expression with FDR < 0.05

Differentially expressed C. rosea milRNAs

 cro-mir-1

68,544

UAGAAUUCGGGGUAGAAU

18

 − 1.83

-0.07

 − 5.84

 cro-mir-2

2032

UAGAAUUCGGGGUAGAAUG

19

 − 2.73

0.49

 − 4.35

 cro-mir-3

33,147

UUAGCCUCGAGACUUUGCA

19

 − 3.74

0.27

 − 4.49

 cro-mir-4

1994

UCAGCCUCGAGACUUUGCC

19

 − 2.92

0.77

 − 6.01

 cro-mir-10

875

UCGGUGGGAUGUUUGAGACU

20

 − 4.74

1.11

 − 3.09

 cro-mir-11

955

UAGAGUUUUUGGAGAUGCU

19

 − 2.42

0.49

 − 6.38

 cro-mir-36

32,160

UCAAACACAAUUAGCGGUC

19

 − 1.9

0.78

 − 6.02

 cro-mir-73^a

48,980

UCUGAAGGUCGUGUGUUC

18

5.65

 − 2.69

 − 2.74

 cro-mir-77^a

683

UAUGCCUAGGCUUGUGCGA

19

 − 3.54

 − 0.93

 − 4.9

 cro-mir-5

94

UUGCAAUGAUUUGCAUUUCGC

21

 − 3.76

 − 2.17

 − 0.88

 cro-mir-6

1875

UAGGACUCGAGUAGUUAUAAC

21

 − 5

0.94

 − 2.47

 cro-mir-9

447

UCGGACGUAUAUUGACUACUC

21

 − 3.79

 − 0.95

 − 4.05

 cro-mir-13

11,099

UUCUUCCUUGAUGCGUCCC

19

 − 4.62

0.11

 − 3.85

 cro-mir-30

187

UGCCUGUCUGAGCGUCAUU

19

 − 2.9

2.15

1.12

 cro-mir-74^a

460

CACGAUGUCCCGUAUCCGACGU

22

 − 2.78

 − 0.73

 − 3.21

 cro-mir-76^a

700

UGUUUCUUUGUUUUUGCCU

19

 − 4.14

0.97

 − 2.46

Differentially expressed Wheat miRNAs

 mir_12061_x13

122

UGUAGAUACUCCCUAAGGCUU

21

 − 1.98

1.71

0.01

 mir_18750_x1

112

UGUAGAUACUCUCUAAGGCUU

21

 − 2.53

2.22

0.48

 mir_16010_x2

114

UGUAGAUACUCCCUAAGGCU

20

 − 2.32

2.01

0.27

 mir_17532_x1

118

UGUAGAUACUCCCUAGGGCUU

21

 − 2.23

1.96

0.15

 mir_19460_x1

125

CACCAACCGGUACUAAUGGGCAUC

24

 − 2.01

2.1

1.55

 mir_13110_x8

172

UCGGACCAGGCUUCAUUCCUU

21

 − 1.51

1.48

0.68

 mir_18139_x1

179

CGCCCCACGGUGGGCGCCA

19

1.65

 − 0.8

 − 0.74

 mir_16988_x1

296

GUGGAUGAUGAGAUCACAAGUAA

23

1.75

 − 0.52

 − 0.95

 mir_15432_x2

140

GCCCCACGGUGGGCGCCA

18

2.34

 − 0.74

 − 1.1

 mir_13653_x6

10,902

GCCCGUCUAGCUCAGUUGGU

20

0.25

 − 1.68

 − 1.5

 mir_16507_x1

83,527

CCGACCUUAGCUCAGUUGGU

20

0.32

 − 1.51

 − 1.31

 mir_18684_x1

201

GACCUGUAUGGGGCACCA

18

0.69

 − 1.9

 − 0.93

 mir_19043_x1

3970

AACCUUGUGGUCGUGGGUUC

20

0.95

 − 1.76

 − 1.39

 mir_15848_x2

30,986

CCCGCCUUGCACCAAGUGAAU

21

 − 0.36

1.54

0.83

 mir_16416_x1

153

CAUCUCUCCUGUAGAAAUAGGCAC

24

 − 0.8

1.56

0.9

 mir_17663_x1

8712

UUUCCCGGCUAGUGCACC

18

 − 0.51

 − 0.44

1.58

 mir_16687_x1

1322

AACUACAAUCUGAGGCUU

18

 − 0.71

0.11

2.42

 mir_18451_x1

689

CCACAGGCUUUCUUGAACUG

20

 − 0.43

0.12

2.51