Posts Tagged ‘comparative genomics’

1000 Fungal Genomes Project

November 11th, 2011


Our proposal to sequence 1000+ fungal genomes has been funded by the Joint Genome Institute (JGI) of the Department of Energy. Our consortium in collaboration with JGI has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life. The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups.

The team comprises Joseph Spatafora (Oregon State University), Jason Stajich (University of California at Riverside), Kevin McCluskey (Fungal Genetics Stock Center), Pedro Crous (Centraal Bureau voor Schimmelcultures, Netherlands), Gillian Turgeon (Cornell University), Daniel Lindner (USDA Forest Service), Kerry O’Donnell and Todd Ward (USDA ARS), Antonis Rokas (Vanderbilt University), Louise Glass (University of California at Berkeley), Betsy Arnold (University of Arizona), Igor Grigoriev (JGI DOE) and myself.

The ‘1000 Fungal Genomes‘ site, set up by Jason Stajich’s group, represents a gathering of the information about the project and will link to additional resources tracking the progress of the project.

Sequencing the Fungal Tree of Life

April 24th, 2011

Last week, a paper of mine has been published online March 14, 2011 in New Phytologist. I enjoyed drafting this letter titled ‘Sequencing the fungal tree of life (fToL)’ with other long-time DOE JGI fungal genomics collaborators. Since I think it is pretty cool, I would like to  further discuss our on-going fToL projects dealing with comparative genomics of soil fungi and metagenomics of forest soils discussed in this paper.

As you may know, forest soils host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon cycling and sequestration, and biogeochemical cycles.

Amongst these microbial communities, soil fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, white- and brown-rot wood decayers, parasites and ectomycorrhizal (ECM) symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga)  remains unexplored using modern high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled ECM, parasite, wood decomposer, litter saprotroph are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, litter decay and mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum.

Thanks to the DOE JGI launched Fungal Genomic Program, the number of available fungal genomes has expanded dramatically in recent months (see my previous post ‘Crunching Fungal Genomes at High Speed‘), and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities. We — David Hibbett, Dan Cullen, Roger Finlay, Cheryl Kuske, Rytas Vilgalys and others — have taken this opportunity to set up a series of projects to elucidate physiological processes taking place along the ‘saprotrophism/mutualism’ continuum encompassing decaying woody debris, soil hyphal networks and ECM symbiosis on major forest ecosystems, using comparative genomics and metatranscriptomic approaches.

As described in the New Phytologist paper, these complementary projects should provide valuable opportunities to investigate two major aspects of the interactions between trees, ECM symbionts and wood/litter decayers, and their role in carbon and nutrient cycling:

  • By studying the transcriptional regulation of genes coding for secreted enzymes, such as plant cell wall polysaccharide degrading enzymes, we would gain a more holistic picture of enzyme secretion and subsequent organic matter turnover than has subsequently been possible.
  • By focusing on transcriptional regulation of fungal genes involved in resource exchange across the ECM/plant and ECM/saprotroph interfaces, we would obtain a better understanding of how mycorrhizal symbiont and the wood decayer communities are altered by changes in nutrient availability.

More exciting times ahead!!!

Another post on this fToL paper: DOE JGI Science Highlights: Toward a Genomic Encyclopedia of Fungi.

F. Martin, D. Cullen, D. Hibbett, A. Pisabarro, J. W. Spatafora, S. E. Baker and I. V. Grigoriev (2011) Sequencing the fungal tree of life. New Phytologist, DOI: 10.1111/j.1469-8137.2011.03688.x

Photo: State Forest of Champenoux © F Martin

Blurred Boundaries

December 4th, 2010

PoplarLaccariaECMOur review paper on the genomes of ectomycorrhizal fungi is available online at the Trends in Genetics site.

Plett JM & Martin F. 2010. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends in Genetics. doi:10.1016/j.tig.2010.10.005

Abstract. “Soils contain a multitude of fungi with vastly divergent lifestyles ranging from saprotrophic to mutualistic and pathogenic. The recent release of many fungal genomes has led to comparative studies that consider the extent to which these lifestyles are encoded in the genome. The genomes of the symbiotic fungi Laccaria bicolor and Tuber melanosporum are proving especially useful in characterizing the genetic foundation of mutualistic symbiosis. New insights gleaned from these genomes, as compared to their saprotrophic and pathogenic cousins, have helped to redefine and shape our understanding of the nature of the symbiotic lifestyle. Here we detail the current state of research into this complex relationship and discuss avenues for future exploration.”

Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA.

JGI Basidiomycete Genome Jamboree

February 24th, 2010

CoprinA Basidiomycete Genomes Jamboree will take place on March 24 – 26, 2010 at the Marriott in Walnut Creek, California, as a satellite meeting of the Annual JGI User Meeting. This jamboree will include brief updates on individual on-going basidiomycete genome projects (Agaricus, Ceriporiopsis, Coprinopsis, Heterobasidion, Melampsora, Pleurotus, Rhodosporidium, Serpula, Tremella) and discussion of comparative genomics of basidiomycete gene families (CAZy, transposable elements, secondary metabolism, pheromones, secretome, transporters).

Progress of the on-going Genome Encyclopedia of Fungi programme will also be discussed.

We will be there to discuss the progress of our own projects.

Photo: Coprinus comatus (the shaggy mane) (© F Martin).

Integrated Microbial Genomes

August 19th, 2009


The Integrated Microbial Genomes (IMG) 2.9 has just been released:

The Integrated Microbial Genomes (IMG) system ( Nucleic Acids Research, 2008, Vol. 36, Database issue ) is a data management, analysis and annotation platform for publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. As today, it contains 1535 bacterial genomes, but only 25 fungal genomes, including 4 basidiomycota.

IMG can be used for finding a genome or a gene, find functions and compare genomes. See the online tutorial at: