TABLE 4.

Endogenous putative gene targets in C. rosea, their expression patterns, and their predicted functions

milRNA identifier	Gene target	Expression log2FCa		Target gene family	Characterized/putative function
		Δdcl2 (Bc)	Δdcl2 (Fg)
cro-mir-3	CRV2G00002264	1.08	1.42	Serine/threonine-protein kinase (Gin4)	Septin ring assembly, intracellular signal transduction
cro-mir-5	CRV2G00013335	1.39	1.25	Unknown	Unknown function
cro-mir-5	CRV2G00015277	2.54	3.52	Transcription factor	60S ribosome biogenesis
cro-mir-10	CRV2G00015277	2.54	3.52	Transcription factor	60S ribosome biogenesis
cro-mir-11	CRV2G00015277	2.54	3.52	Transcription factor	60S ribosome biogenesis
cro-mir-13	CRV2G00001868	1.95	2.72	Helicase	Chromatin remodeling
	CRV2G00002266	1.81	1.98	Transcriptional regulator prz1	Regulates the expression of the Pmc1 ATPase Ca2+ pump
cro-mir-36	CRV2G00013380	2.42	3.36	ATPase	ATPase activity
	CRV2G00005499	1.38	1.8	Unknown	Unknown function
	CRV2G00000111	1.95	2.69	Unknown	Unknown function
	CRV2G00014914	1.21	0.82	Oxidation-reduction process	Part of secondary metabolite BGC
cro-mir-1	CRV2G00003756	1.06	0.89	tRNA ligase	Protein biosynthesis
cro-mir-2	CRV2G00003756	1.06	0.89	tRNA ligase	Protein biosynthesis
cro-mir-3	CRV2G00008014	1.12	0.23	GTPase-activating protein 2	Signal transduction
cro-mir-6	CRV2G00002043	1.12	0.99	Transcription factor	Regulation
cro-mir-3	CRV2G00009307	1.26	0.81	Sterol O-acyltransferase 2	Cholesterol metabolic process
cro-mir-11	CRV2G00009307	1.26	0.81	Sterol O-acyltransferase 2	Cholesterol metabolic process
cro-mir-3	CRV2G00011242	1.26	0.75	Oxidoreductase	Oxidation-reduction
cro-mir-4	CRV2G00011242	1.26	0.75	Oxidoreductase	Oxidation-reduction
cro-mir-13	CRV2G00004332	1.06	0.43	GTP-binding protein	Ribosome biogenesis
cro-mir-1	CRV2G00005300	0.69	1.38	Unknown	Unknown function
cro-mir-4	CRV2G00004339	0.48	1.03	SNF2 RNA helicase	Chromatin remodeling
cro-mir-9	CRV2G00004339	0.48	1.03	SNF2 RNA helicase	Chromatin remodeling
cro-mir-10	CRV2G00004339	0.48	1.03	SNF2 RNA helicase	Chromatin remodeling
cro-mir-11	CRV2G00000903	0.82	1.03	Unknown	Unknown function
cro-mir-36	CRV2G00000903	0.82	1.03	Unknown	Unknown function
cro-mir-10	CRV2G00011823	0.93	1.21	Choline-sulfatase	Hydrolase activity
cro-mir-36	CRV2G00011823	0.93	1.21	Choline-sulfatase	Hydrolase activity
cro-mir-4	CRV2G00012062	−0.18	1.09	Unknown	Unknown function
cro-mir-13	CRV2G00012781	0.3	1.01	Unknown	Unknown function

^aUpregulated (FDR < 0.05 in combination with log₂FC >1) gene targets are highlighted in boldface. Bc, B. cinerea; Fc, F. graminearum.