This page is intentionally left blank APPLIED MYCOLOGY AND BIOTECHNOLOGY VOLUME 4 FUNGAL GENOMICS Edited by Dilip K. Arora Department of Botany Banaras Hindu University India George G. Khachatourians Department of Applied Microbiology and Food Sciences College of Agriculture University of Saskatchewan Saskatoon, SK, Canada ELSEVIER 2004 Amsterdam - Boston - Heidelberg - London - New York - Oxford Paris - San Diego - San Francisco - Singapore - Sydney - Tokyo ELSEVIERB.V. ELSEVIER Inc. ELSEVIERLtd ELSEVIERLtd SaraBurgerhartstraat25 525 B Street, Suite 1900 The Boulevard, Langford Lane 84 Theobalds Road P.O. Box 211,1000 AE San Diego, CA 92101-4495 Kidlington, Oxford OX5 1GB London WC1X 8RR Amsterdam, The Netherlands USA UK UK © 2004 Elsevier B.V. All rights reserved. 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British Library Cataloguing in Publication Data A catalogue record is available from the British Library. ISBN: 0-444-51642-5 @ The paper used in this publication meets the requirements of ANSI/NISO Z39.48-1992 (Permanence of Paper). Printed in The Netherlands. Editors Dilip K. Arora Department of Botany Banaras Hindu University Varanasi, India Fax: +91 542 2368141 Tel:+ 91 542 2369570 E-mail: [email protected] George G. Khachatourians Department of Applied Microbiology and Food Sciences College of Agriculture University of Saskatchewan Saskatoon, Canada Tel: +1 306 966 5032 E- mail: [email protected] Editorial Board Deepak Bhatnagar USDA/ARS, New Orleans, USA Thomas E. Cleveland USDA/ARS, New Orleans, USA Eric A. Johnson University of Wisconsin, Madison, USA Etta Kafer Simon Fraser University, Canada Christian P. Kubicek Technical University of Vienna, Austria B. Franz Lang Universite de Montreal, Canada M. Hyakumachi Gifu University, Japan Mary Anne Nelson University of New Mexico, USA Helena Nevalainen Macquarie University, Australia Nicholas J. Talbot University of Exeter, U.K P. Tudzynski Institut fur Botanik, Munster,Germany This page is intentionally left blank Contents Editorial Board for Volume 4 v Contents vii-viii Contributors ix-xiii Preface xv-xvi The Development of Genetic Markers from Fungal Genome Initiatives 1 Dee A. Carter, Nai Tran-Dinh, Robert E. Marra and Raul E. Vera Inferring Process from Pattern in Fungal Population Genetics 29 Ignazio Carbone and Linda Kohn Molecular and Genetic Basis of Plant-Fungal Pathogen Interactions 59 Seogchan Kang and Katherine F. Dobinson Genomics of Candida albicans 99 Siegfried Salomon, Angelika Felk and Wilhelm Scha'fer Molecular Genetics and Genomics of Phytophthora 137 Susan J. Assinder Genomics of Phytopathogenic Fusarium 161 Haruhisa Suga and Mitsuro Hyakumachi Genomics of Fusarium venenatum: An Alternative Fungal Host for Making 191 Enzymes Randy M. Berka, Beth A. Nelson, Elizabeth J. Zaretsky, Wendy T. Yoder and Michael W. Rey Molecular Characterization of Rhizoctonia solani 205 Mette Liibeck Genomics of Trichoderma 225 Manuel Rey, Antonio Llobell, Enrique Monte, Felice Scala and Matteo Lorito viii Contents Genomics of Economically Significant Aspergillus and Fusarium Species 249 Jiujiang Yu, Robert H. Proctor, Daren W. Brown, Keietsu Abe, Katsuya Gomi, Masayuki Machida, Fumihiko Hasegawa, William C. Merman, Deepak Bhatnagar and Thomas E. Cleveland Penicillium Genomics 285 John C. Royer, Kevin T. Madden, Thea C. Norman and Katherine F. LoBuglio Genomics of Neurospora crassa: From One-Gene-One-Enzyme to 10,000 Genes 295 Edward L. Braun, Donald O. Natvig, Margaret Werner- Washburne and Marry Anne Nelson Genetics and Genomics of Mycosphaerella graminicola: A Model for the 315 Dothideales Stephen B. Goodwin, Cees Waalwijk and Gert H. J. Kema Functional Genomic Analysis of the Rice Blast Fungus Magnaporthe grisea 331 Martin J. Gilbert, Darren M. Soanes and Nicholas J Talbot Genomics of Entomopathogenic Fungi 353 George G. Khachatourians and Daniel Uribe Genomics of Arbuscular Mycorrhizal Fungi 379 Nuria Ferrol, Concepcion Azcon-Aguilar, Bert Bago, Philipp Franken, Armelle Gollotte, Manuel Gonzalez-Guerrero, Lucy Alexandra Harrier, Luisa Lanfranco, Diederik van Tuinen and Vivienne Gianinazzi-Pearson Keyword Index 405 Contributors Keietsu Abe The New Industry Creation Hatchery Center (NICHe), Tohoku University, Sendai 980-8579, Japan. Susan J. Assinder School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, Wales, UK ([email protected]). Concepcion Azcon- Aguilar Estacion Experimental del Zaidin, CSIC, Granada, Spain. Bert Bago Centro de Investigaciones sobre Desertification, CSIC, Valencia, Spain. Randy M. Berka Novozymes Biotech, Inc., 1445 Drew Avenue, Davis, California 95616-4880, USA. Deepak Bhatnagar Food and Feed Safety Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, USA. Edward L. Braun Department of Zoology, University of Florida, Gainesville, Florida 32611, USA. Daren W. Brown Mycotoxin Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois 61604 USA. Ignazio Carbone Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Box 7244 - Partners II Building, Raleigh, NC 27695-7244, USA. Dee A. Carter Discipline of Microbiology, School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia ([email protected]). X Contributors Thomas E. Cleveland Food and Feed Safety Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, USA. Katherine F. Dobinson Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V- 4T3, Canada, and Departments of Biology, Microbiology and Immunology, The University of Western Ontario, London, ON, Canada ([email protected]). Angelika Felk Institute of General Botany, Department of Molecular Phytopathology and Genetics (AMPIII), University of Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany. Nuria Ferrol Estacion Experimental del Zaidin, CSIC, Granada, Spain. Philipp Franken Institute for Vegetable and Ornamental Plants, Grossbeeren, Germany. Martin J. Gilbert School of Biological Sciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter, EX4 4QG, UK. Armelle Gollotte INRA-CMSE, 17 rue Sully-BV154021034, Dijon Cedex, France. Katsuya Gomi The New Industry Creation Hatchery Center (NICHe), Tohoku University, Sendai 980-879, Japan. Manuel Gonzalez-Guerrero Estacion Experimental del Zaidin, CSIC, Granada, Spain. Stephen B. Goodwin U. S. Department of Agriculture, Agricultural Research Service, Department of Botany and Plant Pathology, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA ([email protected]). Lucy Alexandra Harrier The Scottish Agricultural College, Edinburgh, United Kingdom. Fumihiko Hasegawa The New Industry Creation Hatchery Center (NICHe), Tohoku University, Sendai 980-8579, Japan. Mitsuro Hyakumachi Laboratory of Plant Pathology, Faculty of Agriculture, Gifu University, Gifu 501-1193, Japan.