The Ecological Genomics of Fungi

Fungal genomics research has given us a more profound understanding of the vitally important ecological role that fungi play in a diverse array of ecosystems. The Ecological Genomics of Fungi covers a broad diversity of fungal systems and provides unique insights into the functions of those fungi in soil, plant, and human ecosystems. The Ecological Genomics of Fungi brings together the work of leading researchers exploring genomic information on a variety of fungal species. Advances in high–throughput sequencing now offer unprecedented opportunities for identification of novel molecular mechanisms controlling plant–microbe interactions, evolution of fungi, and developmental and ecologically relevant traits. Contributions explore both the positive and negative impacts that fungi bring to an environment, from pathogenesis to symbiosis. The Ecological Genomics of Fungi explores how these massive streams of fungal sequences can be exploited to gain a deeper understanding of the evolution of fungi and their ecological role. Provides timely coverage of the emerging field of ecological genomics and its application to the study of fungi Explores genomics, metagenomics, and metatranscriptomics across a wide range of fungal species Offers unique insight into the functions of fungi in diverse ecosystems, from soil to plant to human Brings together the work of a global team of leading scientists in the field  

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 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

THE EDITOR Francis Martin is the Head of Lab of Excellence for Advanced Research on the Biology of Tree and Forest Ecosystems at the French National Institute for Agricultural Science (INRA).