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Table 6 Major paralogous gene expansions in Trichoderma

From: Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

PFAM domain T. reesei T. virens T. atroviride Other fungia
Unknown protein with ankyrin (PF00023), CCHC zinc finger (PF00098; C-X2-C-X4-H-X4-C) and purine nucleoside phosphorylase domain (01048) 19 38 45 4
Zn(II)Cys6 transcription factor (00172) cluster 1-5 20 43 42 5,1
Peptidase S8 subtilisin cluster 1-4 10 33 36 9,6
Unknown protein with WD40, NACHT and HET domain 13 38 35 3,4
Short chain alcohol dehydrogenase (PF00106) cluster 1 and 2 20 32 34 4,7
Unknown protein family 1-4 12 25 28 5
NAD-dependent epimerase (PFAM 01370) 10 21 23 5,8
Isoflavon reductase, plus PAPA-1 (INO80 complex subunit B), epimerase and Nmr1 domain 9 18 19 6
Ankyrin domain protein 10 17 19 8
Sugar transporters 11 24 18 10,8
GH18 chitinases 6 11 16 2
Protein kinase (00069) plus TPR domain 2 24 15 4,7
Unknown major facilitator subfamily (PF07690) domain 9 15 15 5,5
F-box domain protein 7 10 11 1,7
Ankyrin domain protein with protein kinase domain 6 8 11 2,7
Amidase 4 11 11 2,8
Epoxide hydrolase (PF06441) plus AB hydrolase_1 (PF00561) 5 14 11 3,2
FAD_binding_4, plus HET and berberine bridge enzymes (08031) domain 5 13 11 6,1
FMN oxidoreductases 2 8 10 2,5
Unknown protein with DUF84 (NTPase) and NmrA domain 5 19 10 3,7
Protein with GST_N and GST_C domains 6 12 10 4,6
Class II hydrophobins 6 8 9 1,1
Proteins with LysM binding domains 6 7 9 1,2
Unknown protein family with NmrA domain 2 11 8 0,2
Pro_CA 5 9 8 1,3
WD40 domain protein 5 11 8 2,2
C2H2 transcription factors 1 5 7 1,4
GFO_IDH_MocA (01408 and 02894) oxidoreductase 3 9 7 1,5
Protein kinase (00069) 4 6 6 0,7
Nonribosomal peptide synthase 3 4 5 1
SSCP ceratoplatanin-family 3 4 5 1
GH75 chitosanase 3 5 5 1,1
SNF2, DEAD box helicase 3 5 5 1,3
Nitrilase 3 6 5 2,2
GH65 trehalose or maltose phosphorylase (PFAM 03632) 4 4 4 0,8
AAA-family ATPase (PF00004) 4 3 4 1
Pyridoxal phosphate dependent decarboxylase (00282) 2 3 4 1,2
Unknown protein 3 4 4 1,3
  1. aResults are from MCL analysis of the three Trichoderma species (Tr, Ta, Tv) and mean values from ten other ascomycetes whose genomes are present in the JGI database [63]. Eurotiomycetes: Aspergillus carbonarius, Aspergillus niger. Sordariomycetes: Thielavia terrerstris, Chaetomium globosum, Cryphonectria parasitica, Neurospora discreta, Neurospora tetrasperma. Dothidiomycetes: Mycospherella graminicola, Mycospherella fijiensis, Cochliobolus heterostrophus. The number of genes present in the "other fungi" is averaged. Data were selected from a total of 28,919 clusters, average cluster number 5.8 (standard deviation 15.73). PFAM categories printed in bold specify those that are significantly (P < 0.05) expanded in all three Trichoderma species; numbers in bold and italics specify genes that are significantly more abundant in Ta and Tv versus Tr (P < 0.05). GH, glycosyl hydrolase family; GST, glutahionine-S transferase; SSCP, small secreted cystein-rich protein.