Open Access Highly Accessed Research

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

Christian P Kubicek1*, Alfredo Herrera-Estrella2, Verena Seidl-Seiboth1, Diego A Martinez3, Irina S Druzhinina1, Michael Thon4, Susanne Zeilinger1, Sergio Casas-Flores5, Benjamin A Horwitz6, Prasun K Mukherjee7, Mala Mukherjee6, László Kredics8, Luis D Alcaraz2, Andrea Aerts9, Zsuzsanna Antal8, Lea Atanasova1, Mayte G Cervantes-Badillo5, Jean Challacombe9, Olga Chertkov9, Kevin McCluskey10, Fanny Coulpier11, Nandan Deshpande12, Hans von Döhren13, Daniel J Ebbole14, Edgardo U Esquivel-Naranjo2, Erzsébet Fekete15, Michel Flipphi16, Fabian Glaser6, Elida Y Gómez-Rodríguez5, Sabine Gruber1, Cliff Han9, Bernard Henrissat17, Rosa Hermosa4, Miguel Hernández-Oñate2, Levente Karaffa15, Idit Kosti6, Stéphane Le Crom11, Erika Lindquist9, Susan Lucas9, Mette Lübeck18, Peter S Lübeck18, Antoine Margeot19, Benjamin Metz1, Monica Misra9, Helena Nevalainen12, Markus Omann1, Nicolle Packer12, Giancarlo Perrone20, Edith E Uresti-Rivera5, Asaf Salamov9, Monika Schmoll1, Bernhard Seiboth1, Harris Shapiro9, Serenella Sukno4, Juan Antonio Tamayo-Ramos21, Doris Tisch1, Aric Wiest10, Heather H Wilkinson14, Michael Zhang9, Pedro M Coutinho17, Charles M Kenerley14, Enrique Monte4, Scott E Baker229 and Igor V Grigoriev9

Author Affiliations

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

For all author emails, please log on.

Genome Biology 2011, 12:R40  doi:10.1186/gb-2011-12-4-r40

Published: 18 April 2011

Additional 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.

Format: XLSX Size: 57KB Download file

Open Data

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.

Format: DOCX Size: 38KB Download file

Open Data

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.

Format: DOC Size: 568KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data