TABLE 2.

Differential expression patterns of selected genes in C. rosea Δdcl1 and Δdcl2 mutant strains during interactions with B. cinerea or F. graminearum compared to those of WT C. rosea

Gene ID	Log2FC expressiona				Comment(s)
	Δdcl1 (Bc)	Δdcl1 (Fg)	Δdcl2 (Bc)	Δdcl2 (Fg)
Differentially expressed MFS transporter genes identical to previously characterized MFS transporters
CRV2G00017900	−0.36	−1.94	0.23	−5.05	mfs212 (ID 50% with apdF [PKS-NRPS transport])
CRV2G00017824	0.36	−0.68	0.21	−1.54	mfs (ID 48% OpS2 [Quinone transport])
CRV2G00015530	−0.21	−1.89	0.09	−2.28	mfs (ID 59% with atB [terreic acid transport])
CRV2G00015418	0.02	−1.61	−1.09	−1.56	mfs (ID 60% with FUB11 [polyketide transport])
CRV2G00004817	0.53	−1.6	−4.04	−2.92	mfs506 (ID 57% with FUBT [polyketide transport])
CRV2G00002357	−0.4	−1.26	−1.69	−1.96	mfs533 (ID 70% with rdc3 [polyketide transport])
CRV2G00016200	0.12	−0.69	−2.31	−2.18	mfs530 (ID 60% with rdc3 [polyketide transport])
CRV2G00004939	0.22	−1.76	−2.09	−3.04	mfs534 (ID 80% with rdc3 [polyketide transport])
CRV2G00019617	1.94	4.06	1.59	3	mfs595 (ID 77% with FUS6 [polyketide transport])
CRV2G00011170	0.95	0.17	0.14	−3.32	mfs602 (ID 60% with aflT [polyketide transport])
CRV2G00005334	0.05	−5.44	−4.55	−5.94	mfs589 (ID 70% with aflT [polyketide transport])
Reduced expression of MFS transporters that were induced in C. rosea against B. cinerea or F. graminearum
CRV2G00004685	0.32	−0.79	0.62	−1.57	mfs464
CRV2G00005389	−0.81	−0.75	−1.79	−1.38	mfs271
CRV2G00018263	−0.37	−0.79	−0.74	−2.14	mfs524
CRV2G00011170	−0.03	−1.18	0.14	−3.32	mfs602
CRV2G00012180	1.12	−2.65	−1.45	−2.9	mfs166
CRV2G00015972	−0.06	−2.26	−1.77	−2.3	mfs205
CRV2G00004853	0.45	−1.45	−2.37	−2.27	mfs104
CRV2G00004939	0.22	−1.76	−2.09	−3.04	mfs534
CRV2G00018885	−0.39	−1.22	−3.55	−2.63	mfs24
Differentially expressed polyketide and nonribosomal peptide synthetase genes
CRV2G00011222	−0.67	0.01	0.03	−1.88	pks14
CRV2G00013582	0	−1.43	−0.03	−1.61	pks23
CRV2G00015413	0.75	−2.28	−1.86	−2.96	pks12
CRV2G00015415	1.09	−2.7	−3.22	−3.15	pks2
CRV2G00018696	−0.92	−0.63	−0.13	−4.97	pks6
CRV2G00018222	0.03	−1.43	−2.43	−1.79	pks22
CRV2G00004952	0.11	1.88	0.74	1.54	nrps
CRV2G00005605	0.65	2.73	1.95	2.33	nrps
CRV2G00012656	0.18	1.82	1.95	2.17	nrps16
CRV2G00015275	−0.15	−0.7	0.76	−2.06	nrps
CRV2G00016915	0.67	−1.91	−3.07	−3.17	nrps
CRV2G00014896	0.25	1.44	1.26	1.68	nrps9
CRV2G00005211	0.26	−1.62	−3.74	−2.3	Indole
CRV2G00002084	4.33	0.12	5.24	−0.84	Terpene
Differentially expressed transcription factor genes identical to previously characterized transcription factors
CRV2G00004759	−0.69	−0.32	−1.75	−1.02	ID 60% with FGR27
CRV2G00006707	−0.01	−0.9	−1.62	−1.31	ID 73% with CCAAT-binding subunit HAP3
CRV2G00015419	0.29	−0.95	−2.22	−1.73	ID 53% with sorbicillin regulator YPR2
CRV2G00011734	0.32	1.81	0.56	1.41	ID 79% with abaA
CRV2G00011385	0.19	−0.46	2.58	1.16	ID 57% with CTF1
CRV2G00016352	0.73	1.51	0.47	1.3	ID 65–70% SUC1
CRV2G00019080	1.98	2.1	1.16	1.5	ID 65% with SUC1
CRV2G00019116	0.9	2.32	1.01	2.2	ID 70% SUC1
CRV2G00016935	−0.74	−0.22	−1.69	−0.7	ID 69% with prtT
CRV2G00018531	−0.21	−0.48	−2.12	−1.35	ID 61% with sterol uptake control 2
CRV2G00019093	−0.38	0.43	−1.5	−0.14	ID 60% with GAL4
Differentially expressed chitinases and N-acetylhexosaminidase genes
CRV2G00001280	−0.08	−0.85	−3	−1.67	Chitinase ech42
CRV2G00003425	−0.3	−1.54	−3.6	−3.2	Chitinase ech37
CRV2G00018858	−0.01	−0.06	−1.9	−1.82	Chitinase chia5
CRV2G00017631	−0.07	0.16	0.62	2.51	Chitinase
CRV2G00006887	0.82	2.18	0.92	1.75	Chitinase ech58
CRV2G00011101	−0.3	−0.13	2.25	2.1	Chitinase chic1
CRV2G00002927	−0.21	−0.42	−1.76	−0.78	NAG
CRV2G00012950	−0.14	−0.43	−2.5	−2.26	NAG
Differentially expressed genes associated with gene silencing machinery
CRV2G00000975	0.2	0.1	1.2	1.9	Argonaute2-like
CRV2G00016556	0.2	2.1	0.4	1.3	Chromatin remodeling protein
CRV2G00012165	0.2	4	−0.4	4.3	Histone deacetylase
CRV2G00007951	0.4	0.4	1	1.6	Histone deacetylase
CRV2G00006603	0.9	2.3	2.4	2.3	RNA helicase
CRV2G00007159	0.6	1.6	0.5	1	RNA helicase
CRV2G00001612	−0.6	0.1	−1.6	−1.8	RNA helicase
CRV2G00012613	−0.7	0.9	−2.4	0.1	RNA helicase
CRV2G00009762	0	0.9	−1.7	−0.6	RNA-directed RNA polymerase

^aSignificant differences are indicated in boldface letters. FDR < 0.05 in combination with a log₂ fold change (log₂FC) of >1.5 or <−1.5 was considered to define differentially expressed genes. Bc, B. cinerea; Fc, F. graminearum.