Table 4 Putative C. rosea milRNAs and wheat miRNAs and their putative endogenous and cross-kingdom gene targets of interest. At least two target prediction tools have predicted all putative targets. The plant-based tools psRNATarget, Targetfinder, psROBOT, and TAPIR were used for all putative miRNA-target couples. Moreover, animal-based tools of PITA, Miranda, TargetSpy, and simple seed analysis were utilized through the sRNA toolbox for self-targets of C. rosea milRNAs. All the shown targets also show opposite expressions to the targeting milRNAs (a target needs to be upregulated when the targeting milRNA is downregulated), with Spearman correlation, which is significant, <  − 0.4, and also significantly lesser than the correlation to the average transcript in the same organism. Log2Fc values are in bold when significant (adjusted p-value < 0.05)

Endogenous targets, C. rosea

 cro-mir-36

CRV2T00011673_1

 − 0.94

1.41

1.07

1.59

ABC transporter

Multidrug resistance

 cro-mir-76

CRV2T00005739_1

 − 0.95

3.11

2.91

4.12

Acid phosphatase

Salt stress resistance

 cro-mir-76

CRV2T00021953_1

 − 0.96

3.11

2.97

4.13

Acid phosphatase

Salt stress resistance

 cro-mir-3

CRV2T00011242_1

 − 0.82

0.31

0.52

1.14

Cytochrome P450 monooxygenase

Xenobiotic detoxification and others

 cro-mir-1

cro-mir-2

CRV2T00016330_1

 − 0.9

 − 0.87

0.5

0.48

0.81

MFS transporter

Allantoate permease

 cro-mir-30

CRV2T00004939_1

 − 0.77

2.71

1.98

1.78

MFS transporter 2.A.1.2

Multidrug resistance

 cro-mir-76

CRV2T00009699_1

 − 0.83

0.47

0.26

1.09

MFS transporter 2.A.1.3

Multidrug resistance

 cro-mir-5

CRV2T00017422_1

 − 0.8

9.73

9.1

8.22

Probable apoplastic effector

Unknown

 cro-mir-36

CRV2T00000889_1

 − 0.83

2.03

1.74

1.98

Transcription factor

Glucose-induced endocytosis and carbon catabolite derepression

 cro-mir-3

CRV2T00017200_1

 − 0.91

1.07

0.54

2.16

Transcription factor

Gene expression regulation

 cro-mir-5

CRV2T00000691_1

 − 0.78

0.49

0.7

0.44

Transcription factor

Gene expression regulation

Endogenous targets, wheat

 mir_15432_x2

TraesCS1D01G107100.1

 − 0.77

 − 1.17

 − 0.52

 − 0.20

Mixed-linked glucan synthase 8

Cellulose biosynthesis

 mir_15848_x2

TraesCS3D01G258300.1

 − 0.83

0.32

 − 0.56

 − 0.37

ABC transporter

Unknown

 mir_16507_x1

TraesCS4D01G102700.1

 − 0.82

 − 0.21

0.38

0.42

L-type lectin receptor kinases

Sensing pathogens and activating defense responses

 mir_15432_x2

TraesCS2B01G311600.1

 − 0.77

 − 0.58

 − 0.4

 − 0.48

transport protein Sec24B-like

Vesicle trafficking

 mir_18139_x1

 − 0.76

C. rosea transcripts targeted by wheat miRNAs

 mir_17532_x1

CRV2T00016916_1

 − 0.82

5.63

4.00

4.51

PKS

Synthesis of an antimicrobial compound

 mir_16010_x2

 − 0.85

 mir_12061_x13

 − 0.83