Fungi have a major role in natural ecosystems and in agriculture. This is particularly relevant for fungal species whose main niche is either soil, rhizosphere, plant roots, or above-ground plant tissues. The sequences of fungal genomes provide a new window to observe and understand how fungi recycle organic material in the soil, egngage in positive and negative interactions with plant roots, and attack plants as pathogens. 

This volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens.

In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, and species belonging to Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.

Genomics of Soil-and Plant-Associated Fungi

Genomic Contributions to the Study of Soil and Plant-Interacting Fungi

Benjamin A. Horwitz, Prasun K. Mukherjee, Mala Mukherjee, and Christian P. Kubicek

Fungal Genomics for Energy and Environment

Igor V. Grigoriev

Advancement of Functional Genomics of a Model Species of Neurospora and Its Use for Ecological Genomics of Soil Fungi

Kwangwon Lee and John Dighton

Major Plant Pathogens of the Magnaporthaceae Family

Adriana Illana, Julio Rodriguez-Romero, and Ane Sesma

Aspergillus: Genomics of a Cosmopolitan Fungus

Isabelle Benoit, Iran Malavazi, Gustavo Henrique Goldman, Scott E. Baker, and Ronald P. de Vries

Trichoderma: Genomic Aspects of Mycoparasitism and Biomass Degradation

Christian P. Kubicek and Irina S. Druzhinina

Fusarium oxysporum: A “Moving” View of Pathogenicity

Apratim Chakrabarti

Genomics and Spectroscopy Provide Novel Insights into the Mechanisms of Litter Decomposition and Nitrogen Assimilation by Ectomycorrhizal Fungi

Anders Tunlid, Francois Rineau, Mark Smits, Firoz Shah, Cesar Nicolas, Tomas Johansson, Per Persson, and Francis Martin

Cochliobolus heterostrophus: A Dothideomycete Pathogen of Maize

Benjamin A. Horwitz, Bradford J. Condon, and B. Gillian Turgeon

Penicillium chrysogenum: Genomics of an Antibiotics Producer

Marco A. van den Berg

Rhizopus oryzae: Genetic Secrets of an Emerging Human Pathogen

Brian L. Wickes

Podospora anserina: From Laboratory to Biotechnology

Philippe Silar

Recent Advances on the Genomics of Litter- and Soil-Inhabiting Agaricomycetes

Phil Kersten and Dan Cullen

Archaeorhizomycetes: Patterns of Distribution and Abundance in Soil

Anna Rosling, Ina Timling, and D. Lee Taylor

Methods in Fungal Genetics

Kevin McCluskey and Aric Wiest