Research
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
1 Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
2 Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
3 Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA
4 Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
5 División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
6 Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
7 Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
8 Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
9 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
10 School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
11 Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
12 Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
13 TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany
14 Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
15 Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
16 Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain
17 Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
18 Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
19 Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France
20 Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
21 Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
22 Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
Genome Biology 2011, 12:R40 doi:10.1186/gb-2011-12-4-r40
Published: 18 April 2011Additional files
Additional file 1:
Comparative properties and gene inventory of T. reesei, T. virens and T. atroviride. This file contains additional information on genomic properties and selected gene families from the three Trichoderma species comprising 19 tables. Table S1 summarizes the satellite sequences identified in the Trichoderma genomes and four other fungal genomes. Table S2 summarizes manually curated sequence alignments of transposable element families from the Trichoderma genomes. Table S3 lists the total number of CAZy families in Trichoderma and other fungi. Table S4 lists the glycoside hydrolase (GH) families in Trichoderma and other fungi. Table S5 lists the glycosyltransferase (GT) families in Trichoderma and other fungi. Table S6 lists the polysaccharide lyase (PL) families in Trichoderma and other fungi. Table S7 lists the carbohydrate esterase (CE) families in Trichoderma and other fungi. Table S8 lists the carbohydrate-binding module (CBM) families in Trichoderma and other fungi. Table S9 lists the NRPS, PKS and NRPS-PKS proteins in T. atroviride. Table S10 lists NRPS, PKS and NRPS-PKS proteins in T. virens. Table S11 lists the putative insecticidal toxins in Trichoderma. Table S12 lists the cytochrome P450 CYP4/CYP19/CYP26 class E proteins in Trichoderma. Table S13 lists the small-cysteine rich secreted protein from Trichoderma spp. Table S14 lists the most abundant PFAM domains in those genes that are unique to T. atroviride and T. virens and not present in T. reesei. Table S15 surveys the assembly statistics. Table S16 provides gene model support. Table S17 summarizes gene model statistics. Table S18 provides numbers of genes with functional annotation according to KOG, Gene Ontology, and KEGG classifications. Table S19 lists the largest KOG families responsible for metabolism.
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Additional file 2:
Additional information on selected gene groups of Trichoderma, methods used for genome sequencing, and legends for the figures in Additional file 3. Chapter 1: Carbohydrate-Active enzymes (CAZymes). Chapter 2: Aegerolysins and other toxins. Chapter 3: Small secreted cysteine rich proteins (SSCPs). Chapter 4: EST sequencing and analysis. Chapter 5: Legends to figures.
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Additional file 3:
Figures that illustrate selected aspects of the main text. Figure S1 provides a phylogeny of Trichoderma NPRSs. Figure S2 compares the numbers of epoxide hydrolase genes in Trichoderma with that in other fungi. Figure S3 compares the codon usage in genes from syntenic and nonsyntenic regions of the genomes of Trichoderma reesei, T. atroviride and T. virens.
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