Sequencing the fungal tree of life.

Terrestrial ecosystems host a complex array of interacting communities, with thousands of species of animals, plants, fungi and bacteria. In soils, this complex web of life is responsible for the cycling of carbon (C), for water and nutrients, for soil quality and for plant nutrition and health. To predict future changes of these threatened ecosystems and to fully grasp the biological and chemical workings of these complex interactions, one must not only regard organisms as individuals but also as members of a larger community, considering the interplay and communication between individuals within these entangled populations, that is, their extended phenotype (Whitham et al., 2008). One emerging model for such studies is the interaction between soil-borne fungi and plant communities. Fungi are one of the largest and most diverse kingdoms of eukaryotes and function as important biological components of all terrestrial ecosystems. They are central to the global C cycle, constitute the major group of plant pathogens in managed and natural ecosystems, serve as symbionts with heterotrophic and autotrophic organisms alike, and play an integral and growing role in the development and production of renewable bio-based fuels and chemicals. The success and importance of fungi to life on Earth are directly attributable to the remarkable diversity of enzymes and metabolites that they produce, which afford them a broad range of nutritional modes and grant them access to an amazing breadth of C sources and ecological niches. Understanding how saprotrophic, symbiotic and pathogenic fungi achieve their lifestyle is crucial for understanding their ecological functions and their subsequent impact on the fate of plant communities. The inconspicuous nature of soil fungi, the inaccessibility of their habitats and our inability to culture many of them have made them difficult to study. Advances in large-scale DNA barcoding surveys have circumvented some of these limitations and allowed us to determine the composition and the dynamics of several fungal soil communities, including mycorrhizal fungi (Buée et al., 2009; Öpik et al., 2009; Jumpponen et al., 2010). Several hundred species are active in soils, and ongoing metagenomics and metatranscriptomics studies will uncover the functions encoded in their genomes as well as their expressed transcripts (Martin &Martin, 2010). Many of the fungi whose genomes have been sequenced are residents of soil and plants (Martinez et al., 2004, 2009; Martin et al., 2008, 2010; Ohm et al., 2010; Spanu et al., 2010; Stajich et al., 2010) and these sequences will provide baseline genomic information that enables scientists to explore the genomes and functions of thousands of soil fungal species that cannot be cultured and sequenced directly. Unfortunately, reference fungal genomes sequenced to date, and those in progress, show significant bias towards fungi of medical importance (Cuomo & Birren, 2010). The availability of genome sequences from ecologically and taxonomically diverse fungi not only would allow ongoing research on those species, but enhances the value of other sequences through comparative studies of gene evolution, genome structure, metabolic and regulatory pathways, and saprotrophism ⁄ symbiosis ⁄pathogenesis lifestyles. Recently, the US Department of Energy Joint Genome Institute (JGI) launched the Fungal Genomics Program (FGP), aimed at exploration of fungal diversity for energy and environmental sciences and applications through the scale-up of sequencing and analysis (Grigoriev et al., 2011).