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Front Matter The Ecological Genomics of Fungi The Ecological Genomics of Fungi Editor FRANCIS MARTIN This edition first published 2014 © 2014 by John Wiley & Sons, Inc Editorial Offices 1606 Golden Aspen Drive, Suites 103 and 104, Ames, Iowa 50010, USA The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 9600 Garsington Road, Oxford, OX4 2DQ, UK For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Blackwell Publishing, provided that the base fee is paid directly to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license by CCC, a separate system of payments has been arranged. The fee codes for users of the Transactional Reporting Service are ISBN-13: 978-1-1199-4610-6/2014. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. Limit of Liability/Disclaimer of Warranty: While the publisher and author(s) have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. It is sold on the understanding that the publisher is not engaged in rendering professional services and neither the publisher nor the author shall be liable for damages arising herefrom. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloging-in-Publication Data The ecological genomics of fungi / editor, Francis Martin. pages cm Includes bibliographical references and index. ISBN 978-1-119-94610-6 (cloth : alk. paper) – ISBN 978-1-118-72970-0 (epub) – ISBN 978-1-118-72971-7 (epdf) – ISBN (invalid) 978-1-118-72972-4 (emobi) – ISBN 978-1-118-73589-3 (ebook) 1. Fungi–Genetics. 2. Genomics. 3. Ecology. I. Martin, Francis, 1954– editor of compilation. QK602.E26 2014 571.5′92–dc23 2013029869 A catalogue record for this book is available from the British Library. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Cover images: © Francis Martin Cover design by Nicole Teut Set in 10.5/12pt Times by SPi Publisher Services, Pondicherry, India 1 2014 Contents Contributors vii Preface xiii Section 1 Sequencing Fungal Genomes 1 1 A Changing Landscape of Fungal Genomics 3 Igor V. Grigoriev 2 Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi 21 Claude Murat, Thibaut Payen, Denis Petitpierre, and Jessy Labbé Section 2 Saprotrophic Fungi 41 3 Wood Decay 43 Dan Cullen 4 Aspergilli and Biomass-Degrading Fungi 63 Isabelle Benoit, Ronald P. de Vries, Scott E. Baker, and Sue A. Karagiosis 5 Ecological Genomics of Trichoderma 89 Irina S. Druzhinina and Christian P. Kubicek Section 3 Plant-Interacting Fungi 117 6 Dothideomycetes: Plant Pathogens, Saprobes, and Extremophiles 119 Stephen B. Goodwin 7 Biotrophic Fungi (Powdery Mildews, Rusts, and Smuts) 149 Sébastien Duplessis, Pietro D. Spanu, and Jan Schirawski 8 The Mycorrhizal Symbiosis Genomics 169 Francis Martin and Annegret Kohler 9 Lichen Genomics: Prospects and Progress 191 Martin Grube, Gabriele Berg, Ólafur S. Andrésson, Oddur Vilhelmsson, Paul S. Dyer, and Vivian P.W. Miao v vi CONTENTS Section 4 Animal-Interacting Fungi 213 10 Ecogenomics of Human and Animal Basidiomycetous Yeast Pathogens 215 Sheng Sun, Ferry Hagen, Jun Xu, Tom Dawson, Joseph Heitman, James Kronstad, Charles Saunders, and Teun Boekhout 11 Genomics of Entomopathogenic Fungi 243 Chengshu Wang and Raymond J. St. Leger 12 Ecological Genomics of the Microsporidia 261 Nicolas Corradi and Patrick J. Keeling Section 5 Metagenomics and Biogeography of Fungi 279 13 Metagenomics for Study of Fungal Ecology 281 Björn D. Lindahl and Cheryl R. Kuske 14 Metatranscriptomics of Soil Eukaryotic Communities 305 Laurence Fraissinet-Tachet, Roland Marmeisse, Lucie Zinger, and Patricia Luis 15 Fungi in Deep-Sea Environments and Metagenomics 325 Stéphane Mahé, Vanessa Rédou, Thomas Le Calvez, Philippe Vandenkoornhuyse, and Gaëtan Burgaud 16 The Biodiversity, Ecology, and Biogeography of Ascomycetous Yeasts 355 Marc-André Lachance Index 371 Contributors Ólafur S. Andrésson Institute of Life and Environmental Sciences University of Iceland Reykjavik, Iceland Scott E. Baker Pacific Northwest National Laboratory Richland, Washington Isabelle Benoit CBS-KNAW Fungal Biodiversity Centre Utrecht, The Netherlands Gabriele Berg Institute for Environmental Biotechnology Graz University of Technology Graz, Austria Teun Boekhout CBS-KNAW Fungal Biodiversity Centre Utrecht, The Netherlands Gaëtan Burgaud Laboratoire Universitaire de Biodiversité et Ecologie Microbienne Université Européenne de Bretagne Université de Brest ESIAB Technopôle Brest-Iroise Plouzané, France Nicolas Corradi Canadian Institute for Advanced Research Department of Biology University of Ottawa Ontario, Canada vii viii CONTRIBUTORS Dan Cullen Forest Products Laboratory Madison, Wisconsin Tom Dawson Procter & Gamble Co. Cincinnati, Ohio Ronald P. de Vries CBS-KNAW Fungal Biodiversity Centre Utrecht, The Netherlands Irina S. Druzhinina Research Area Biotechnology and Microbiology Institute of Chemical Engineering Vienna University of Technology Vienna, Austria and Austrian Center of Industrial Biotechnology Institute of Chemical Engineering Vienna University of Technology Vienna, Austria Sébastien Duplessis Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France Paul S. Dyer School of Biology University of Nottingham Nottingham, United Kingdom Laurence Fraissinet-Tachet Ecologie Microbienne, UMR CNRS 5557 – USC INRA 1364 Université de Lyon Université Lyon 1, Villeurbanne, France Stephen B. Goodwin USDA-ARS Crop Production and Pest Control Research Unit Department of Botany and Plant Pathology Purdue University West Lafayette, Indiana Igor V. Grigoriev US Department of Energy Joint Genome Institute Walnut Creek, California CONTRIBUTORS ix Martin Grube Institut für Pflanzenwissenschaften Karl-Franzens-Universität Graz Graz, Austria Ferry Hagen Department of Medical Microbiology and Infectious Diseases Canisius Wilhelmina Hospital Nijmegen, The Netherlands Joseph Heitman Department of Molecular Genetics and Microbiology Duke University Medical Center Durham, North Carolina Sue A. Karagiosis Pacific Northwest National Laboratory Richland, Washington Patrick J. Keeling Canadian Institute for Advanced Research Department of Botany University of British Columbia Vancouver, Canada Annegret Kohler Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France James Kronstad Michael Smith Laboratories Department of Microbiology and Immunology University of British Columbia Vancouver, Canada Christian P. Kubicek Research Area Biotechnology and Microbiology Institute of Chemical Engineering Vienna University of Technology Vienna, Austria and Austrian Center of Industrial Biotechnology Institute of Chemical Engineering Vienna University of Technology Vienna, Austria x CONTRIBUTORS Cheryl R. Kuske Environmental Microbiology Team Bioscience Division Los Alamos National Laboratory Los Alamos, New Mexico Jessy Labbé BioSciences Division Oak Ridge National Laboratory Oak Ridge, Tennessee Marc-André Lachance Department of Biology University of Western Ontario London, Ontario, Canada Thomas Le Calvez Université de Rennes 1, CNRS, UMR6553 EcoBio Observatoire Des Sciences de l’Univers de Rennes (OSUR) Campus de Beaulieu Rennes, France Björn D. Lindahl Swedish University of Agricultural Sciences Department of Forest Mycology and Plant Pathology Uppsala, Sweden Patricia Luis Ecologie Microbienne, UMR CNRS 5557 – USC INRA 1364 Université de Lyon Université Lyon 1, Villeurbanne, France Stéphane Mahé Université de Rennes 1, CNRS UMR6553 EcoBio Observatoire Des Sciences de l’Univers de Rennes (OSUR) Campus de Beaulieu Rennes, France Roland Marmeisse Ecologie Microbienne, UMR CNRS 5557 – USC INRA 1364 Université de Lyon Université Lyon 1, Villeurbanne, France CONTRIBUTORS xi Francis Martin Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France Vivian P.W. Miao Department of Microbiology and Immunology University of British Columbia Vancouver, Canada Claude Murat Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France Thibaut Payen Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France Denis Petitpierre Laboratory of Excellence ARBRE UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes INRA-Nancy Champenoux, France Vanessa Rédou Laboratoire Universitaire de Biodiversité et Ecologie Microbienne Université
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