Genome Sequencing and Analysis of the Biomass-Degrading Fungus Trichoderma reesei (syn. Hypocrea jecorina)

Authors

• Diego Martinez, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Randy M. Berka, Novozymes, Inc., 1445 Drew Ave., Davis, California
• Bernard Henrissat, AFMB UMR 6098, CNRS, Universite´s d’Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France
• Markku Saloheimo, VTT Technical Research Centre of Finland, Tietotie 2, Espoo, PO Box 1000, 02044 VTT-Espoo, Finland
• Mikko Arvas, VTT Technical Research Centre of Finland, Tietotie 2, Espoo, PO Box 1000, 02044 VTT-Espoo, Finland.
• Scott E. Baker, Pacific Northwest National Laboratory, PO Box 999, Richland, Washington
• Jarod Chapman, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California 94598, USA
• Olga Chertkov, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Pedro M. Coutinho, AFMB UMR 6098, CNRS, Universite´s d’Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France
• Dan Cullen, United States Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Dr., Madison, Wisconsin 53726, USA
• Etienne G. J. Danchin, AFMB UMR 6098, CNRS, Universite´s d’Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France
• Igor V. Grigoriev, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California 94598, USA
• Paul Harris, Novozymes, Inc., 1445 Drew Ave., Davis, California
• Melissa Jackson, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Christian P. Kubicek, Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Technische Universitaet Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
• Cliff S. Han, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Isaac Ho, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California 94598, USA.
• Luis F. Larrondo, Departmento de Gene´ tica Molecular y Microbiologı´a, Facultad de Ciencias Biolo´ gicas, Pontifica Universidad Cato´ lica de Chile and Millennium lnstitute for Fundamental and Applied Biology, Santiago, Chile
• Alfredo Lopez de Leon, Novozymes, Inc., 1445 Drew Ave., Davis, California
• Jon K. Magnuson, Pacific Northwest National Laboratory, PO Box 999, Richland, Washington 99352, USA
• Sandy Merino, Novozymes, Inc., 1445 Drew Ave., Davis, California
• Monica Misra, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Beth Nelson, Novozymes, Inc., 1445 Drew Ave., Davis, California
• Nicholas Putnam, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Barbara Robbertse, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
• Asaf A. Salamov, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Monika Schmoll, Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Technische Universitaet Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
• Astrid Terry, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Nina Thayer, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Ann Westerholm-Parvinen, VTT Technical Research Centre of Finland, Tietotie 2, Espoo, PO Box 1000, 02044 VTT-Espoo, Finland
• Conrad L. Schoch, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
• Jian Yao, Genencor International, 925 Page Mill Road, Palo Alto, California 94304, USA
• Ravi Barabote, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Mary Anne Nelson, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
• Chris Detter, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• David Bruce, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Cheryl R. Kuske, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Gary Xie, Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico
• Paul Richardson, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Daniel S. Rokhsar, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Susan M. Lucas, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Edward M. Rubin, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California
• Nigel Dunn-Coleman, AlerGenetiCa SL, Santa Cruz, Tenerife, Spain
• Michael Ward, Genencor International, 925 Page Mill Road, Palo Alto, California 94304, USA
• Thomas Brettin, Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California

Date of this Version

5-2008

Comments

Published in NATURE BIOTECHNOLOGY VOLUME 26, NUMBER 5, MAY 2008.

Abstract

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.