Evolution and comparative genomics of the most common Trichoderma species

Kubicek, Christian P.; Steindorff, Andrei S.; Chenthamara, Komal; Manganiello, Gelsomina; Henrissat, Bernard; Zhang, Jian; Cai, Feng; Kopchinskiy, Alexey G.; Kubicek, Eva M.; Kuo, Alan; Baroncelli, Riccardo; Sarrocco, Sabrina; Noronha, Eliane Ferreira; Vannacci, Giovanni; Shen, Qirong; Grigoriev, Igor V.; Druzhinina, Irina S.

doi:10.1186/s12864-019-5680-7

BMC Genomics

Table 4 PFAM group members with more than 500 genes in the 13 Trichoderma isolates

From: Evolution and comparative genomics of the most common Trichoderma species

		clusters	genes per cluster	total genes	genes/ species	HV/SL^a	HV/ST^a	ST/SL^a	singletons^b	multiples^c	C/S^d (%)
Zn2Cys6 transcriptional regulators	PF04082	238	12.3	2929	225.3	1.69	1.21	1.40	84	154	64.7
MFS permeases	PF07690	172	17.3	2972	228.6	1.55	1.06	1.46	67	105	61.0
short-chain dehydrogenases/reductases	PF00106	121	17.6	2129	163.8	1.68	1.18	1.42	46	75	62.0
ankyrin-containing proteins	PF00023	106	14.4	1524	117.2	1.84	1.05	1.75	20	86	81.1
alpha-beta-hydrolases	PF00561, 07859, 02230	96	14.4	1382	106.3	2.02	1.27	1.59	29	67	69.8
protein kinases	PF00069	98	12.4	1218	93.7	1.15	1.11	1.03	60	38	38.8
zinc-dependent alcohol dehydrogenases	PF00107	66	17.6	1159	89.2	1.89	1.17	1.61	15	51	77.3
FAD-binding oxidases	PF01494, 01565	84	13.8	1158	89.1	1.56	1.21	1.29	25	59	70.2
methyltransferases	PF00891	91	12.7	1157	89.0	1.24	1.09	1.14	46	45	49.5
AAA + -ATPasesAAA+ − ATPases	PF00004	85	13.3	1130	86.9	1.13	1.06	1.07	54	31	36.5
cytochrome P450 monooxygenases	PF00067	59	15.9	940	72.3	1.65	1.69	0.97	14	45	76.3
sugar transporters	PF00083	65	14.2	923	71.0	1.53	1.17	1.31	33	32	49.2
ABC-transporters	PF00005	48	16.3	780	60.0	1.22	1.13	1.07	21	27	56.3
vegetative heteroincompatibility (HET) proteins	PF06985, 07217, 17,108	72	10.5	753	57.9	1.94	1.24	1.56	13	59	81.9
aminotransferases	PF01490	49	13.8	675	51.9	1.47	1.18	1.25	21	28	57.1
amino acid permeases	PF00324	48	13.1	630	48.5	1.17	1.10	1.06	30	18	37.5
amidases	PF01979, 04909	37	17.0	629	48.4	1.93	1.20	1.62	12	25	67.6
acetytransferase	PF00583, 00797, 13,302, 13,523	49	12.2	600	46.2	1.26	1.10	1.15	23	26	53.1
DEAD-box helicases	PF00270	42	13.5	567	43.6	0.97	0.96	1.01	33	9	21.4
NmrA-like proteins, NAD-binding negative regulators of GATA-binding proteins	PF05368	41	13.5	552	42.5	3.01	1.11	2.70	10	31	75.6
DnaJ molecular chaperone	PF00226	42	12.8	537	41.3	1.02	0.99	1.04	19	23	54.8
RRM_1 RNA binding proteins	PF00076	42	12.8	537	41.3	1.00	0.99	1.01	40	2	4.8

^a -ratio of the number of genes in all species belonging to one of the Trichoderma sections or clades
^b - genes which are present in one a single copy per cluster
^c - genes that occur in more than one copy per cluster in at least one species
^d - percentage of clusters containing multiple genes

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ISSN: 1471-2164

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