Posts Tagged ‘basidiomycetes’

Basidiomycete Genome Meeting

December 19th, 2010

FomitopsisIgor Grigoriev, David Hibbett and I are organizing a one-day workshop on March 21, 2011 at the JGI in Walnut Creek to cover comparative genome analysis of basidiomycetes. This jamboree will take place between the Fungal Genetics Conference in Asilomar (Mar 15-20) and the JGI User Meeting (Mar 22-24). The workshop will  include sessions on wood decayers, symbionts and soil fungal metagenomics.

The various sessions will include an update on current genome sequencing projects running at the JGI, including the Wood Decayers and Mycorrhizal Symbionts projects, and cross-all-basidio comparisons.

People willing to make a contribution can contact Igor, David or myself.

Photo: Early stages of Fomitopsis fruiting body development. Spruce forest near Pierre Percée in the Vosges range. © F Martin

Heading to Walnut Creek

March 20th, 2010

Fomitopsis pinicolaNext week a collection of international ‘afficionados’ exploring fungal genomes will be meeting in Walnut Creek (in the Bay  Area) at the JGI Basidiomycetes Jamboree.  I am hopeful we’ll come up with some strategies and principles that can guide how the increasing number of fungal genomes (e.g. Agaricus, Pleurotus, Serpula, Pisolithus, Paxillus)  can be more effectively mined and the resulting comparative analyses provided to mycologists and scientists interested by the eukaryote evolution (see also Jason’s blog post: ‘Preparing for meeting on Fungal Genome databases‘) . I expect that we will also be discussing how genome databases can be interconnected to facilitate comparative analyses between groups. The JGI Fungal Genome Initiative and the Genoscope DIKARYOME projects will likely generate >100 genomes of yeast and filamentous fungal genomes in the next two years. Added to the 200 currently available genomes, these novel genome sequences will undoubtly facilitate our understanding of  the  life history of Mycota and help us to explain their tremendous ability to colonize most ecosystems on Earth. I will keep you in the loop.

Photo:  Red-belted Polypore (Fomitopsis pinicola) © FM

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).

The Genome Encyclopedia of Fungi

October 18th, 2009

jgiBecause of the importance of fungi to Department of Energy (DOE) mission areas such bioenergy production, bioremediation and carbon cycling, the Joint Genome Institute has decided to develop a formal Fungal Genomics Program. In bioenergy projects alone, for example, fungal genome data have been used not only to ensure the health of crops that serve as biomass feedstocks (e.g., Poplar/Melampsora interaction) but also provide enzymes that can break down the biomass. Currently, the vast majority of fungi whose genomes have been sequenced are ascomycetes and basidiomycetes. The result of this bias is that we don’t have a grasp of the enzymatic and metabolic diversity found in the fungal kingdom. The JGI has thus developed a Fungal Genomics Program headed by Igor Grigoriev. The program’s first project, launched October 1, is the Genome Encyclopedia of Fungi (GEF). The program aims to explore fungi’s ecological diversity and breadth across the Tree of Life. One thrust area will be devoted to basidiomycetes. Another thrust area of this program will aim to sequence genomes across the fungal tree of life.  Additional thrust areas will be aimed at in depth sequencing of other fungal groups that are key to DOE mission areas, such as the Dothideomycetes.

hc2Years 2009 and 2010 will be devoted to building and piloting a fungal genome sequencing pipeline that scales – from DNA sample preparation to automated annotation to comparative genomics tools. Five genomes will initially sequenced per month. Within the candidate basidiomycetes for sequencing there are several soil fungi involved in wood degradation and ectomycorrhizal symbiosis, including Gloeophyllum trabeum (brown-rot), Fomitiporia mediterranea (white-rot), and Hebeloma cylindrosporum (symbiont). These multiple genomes will allow a thorough comparative analysis of the genome traits underlying the fungal lifestyles.