The Ecological Genomics of Fungi

This unique book covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems – from soil, to plant, to human. Bringing together fungal genomic information on a variety of lifestyles and traits, the book covers saprotrophism, pathogenesis (including biotrophs, hemibiotrophs, necrotrophs) and symbiosis. Advances in high-throughput sequencing now offer unprecedented opportunities for identification of novel key molecular mechanisms controlling plant-microbe interactions, evolution of fungi and developmentally- and ecologically-relevant traits, this book 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.

Although tremendous progress has been made in recent years in fungal genomics, thanks to the sequencing of over one hundred fungal genomes, until now no book has used this information to bridge fungal genomics, molecular ecology and ecology. Edited by a recognized leader in fungal genomics and soil metagenomics with over a decade of experience, Genomics & Metagenomics for Harnessing the Ecology of Fungi will be a useful resource for the experienced as well as the new researchers entering 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

“I think the volume may succeed in its ambition to serve as a catalyst for further studies by showing researchers venturing into ecological genomics and those already in genomics the width of the field. This may, in turn, further more integrative studies that will benefit our understanding of fungi.” (The Quarterly Review of Biology, 1 October 2015)

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).

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