Archive for October, 2009

Future Microbiome Projects

October 25th, 2009

A significant part of JGI FY 2010 funding will be aimed to projects of interest to our lab. This includes:

• A Great Prairie soil metagenome project that Jim Tiedje of Michigan State University is leading with Janet Jansson of Lawrence Berkeley National Laboratory.
• An Arabidopsis rhizosphere project led by JGI microbial ecology group leader Phil Hugenholtz and Jeff Dangl of the University of North Carolina at Chapel Hill.

The Smell of Autumn

October 25th, 2009

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Fall was so dry that mushrooms remained rare in the woods around the village. I missed the long walks through the trees hunting the fruits of the underground fungal webs. Mid-October finally brought rain and mushrooms poped up, but most of them are saprotrophs efficiently eating wood logs and dead stumps. When seeing this silent but frenetic activity I realized why so many are in the Genome Encyclopedia of Fungi portfolio.

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.