November 8th, 2009 by Francis Martin
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The JGI have announced the pre-release of the Agaricus bisporus var. bisporus (H97) v1.0 assembly. The genome size is 30.2 Mbp with an average coverage of 8.5x. based on ab initio prediction, protein alignment and ESTs, ~10,000 genes have been predicted by automated annotation. The annotation may be browsed, searched, downloaded and expanded with your curations at the Agaricus bisporus var. bisporus (H97) portal: genome.jgi-psf.org/Agabi1. Because this is a pre-release only approved users will be able to get access to this portal.
Cartoon: © www.mssf.org
October 25th, 2009 by Francis Martin
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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.
October 25th, 2009 by Francis Martin
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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.
October 18th, 2009 by Francis Martin
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Because 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.
Years 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.
September 29th, 2009 by Francis Martin
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The tree-killing fungus Grosmannia clavigera (= Ophiostoma clavigerum) carried by the mountain pine beetle (MPB), Dendroctonus ponderosae, is devastating pine forests in British Columbia (Canada). This sap-stain ascomycetous fungus grows rapidly in the host tree phloem and through the sapwood where it produces melanin that discolours the wood, and blocks the host tree’s water transport system. More than 15 million hectares of pine forests are currently affected by MPB. The pathogenic fungus recently crossed the Rocky Mountains into Alberta, raising the concern that pine forests across Canada may become affected. Bark beetles, beetle-associated tree-infecting fungi, and pine trees are three of the major interacting biological components of this epidemic. Genomics offers new approaches to delineate some of these complex biological interactions (see the TRIA project web site for details). Scott DiGuistini and his collaborators have combined combined conventional, 40-kb fosmid paired-end Sanger reads from an ABI 3730xl sequencer, single-end 454 reads from Roche GS20 and GS FLX sequencers, and paired-end reads from an Illumina Genome Analyzer sequencer for generating the ~32.5 Mb draft genome sequence of G. clavigera. They developed a hybrid approach that uses the Forge and Velvet assemblers for generating the de novo draft genome sequences. This G. clavigera genome sequencing, together with the sequencing of the methylotrophic yeast Pichia pastoris, demonstrate that the new sequencing technologies can efficiently be used for generating genome draft for eukaryotic fungal genomes.
Scott DiGuistini et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology 10: R94
September 20th, 2009 by Francis Martin
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A large international research team lead by Sophien Kamoun (Sainsbury Lab) and the Broad Institute (Brian Haas & Chad Nusbaum et al.) has decoded the genome of Phytophthora infestans that triggered the Irish potato famine in the mid-19th century and now threatens this season’s tomato and potato crops. This water mold, which is more closely related to the malaria parasite than to fungi, thrives in cool, wet weather, and can infect potatoes, tomatoes and other related plants, causing a “late blight” disease that can decimate entire fields in just a few days.
The genome sequence was reported in Nature. The genome of this fungus-like Oomycete — related to brown algae — is very large (~240 Mb; other species in the Phytophthora genus have less than 100 Mb). The genome analysis revealed a ‘two-speed’ genome, meaning that different parts of the genome are evolving at different rates. The pathogen can adapt rapidly to the plant immune system thanks to its genomic features including:
- alternating repeat-rich (and gene-poor) regions and gene-dense regions;
- gene-dense regions are shared among other Phytophthora species, preserved over millions of years of evolution, whereas the repeat-rich regions are undergoing relatively rapid changes;
- The repeat-rich regions contain fewer genes compared to other genomic regions, yet those genes they do contain are enriched for those that play crucial roles in plant infection. The latter include small secreted proteins with a RXLR motif involved in the in planta targeting and CRN genes.
Further studies of these pathogenesis-related effectors will foster a deeper understanding of plant infection and help identify potential targets for environment-friendly protection treatments.
You can also listen to Sophien discuss his work in the September 10 issue Nature Podcast. He provides some good background and makes some suggestions as to how the genome can help with protecting potatoes.
September 20th, 2009 by Francis Martin
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Fungal interactions with plant roots are of major ecological and economic importance. They include beneficial interactions, such as the mutualistic mycorrhizal symbiosis, but also numerous detrimental interactions induced by soilborne pathogens. The root-rot pathogenic fungus Nectria haematococca, belonging to the ‘‘Fusarium solani species complex’’, is a common soil saprotroph and plant pathogen also causing opportunistic infections in animals, including man. F. solani is also damaging the prehistorical paintings of the caves at Lascaux. The ecological and host diversity of the fungus N. haematococca has been shown to be due in part to unique genes on different supernumerary chromosomes. These “extra” chromosomes are called “conditionally dispensable” (CD) chromosomes because while they are not required for axenic growth, they may allow isolates to have an expanded host range. The PDA1-CD chromosome carries a cluster of genes for pea pathogenicity. The 54 Mb genome of N. haematococca has been sequenced by the Joint Genome Institute and a paper in PLoS Genetics reports the major features of this genome. The current study reveals that it has one of the largest fungal genomes (15,707 genes), which may be related to its habitat diversity, and describes two additional supernumerary chromosomes. Two classes of genes were identified that have contributed to gene expansion: 1) lineage-specific genes (that are not found in other fungi), and 2) genes that are present as multiple copies in N. haematococca but commonly occur as a single copy in other fungi. Some of these genes have properties suggesting their acquisition by horizontal gene transfer. VanEtten and his colleagues showed that the three supernumerary chromosomes are different from the normal chromosomes; they contain more repeat sequences, are particularly enriched in unique and duplicated genes, and have a lower G+C content. In addition, the biochemical functions encoded by genes on these chromosomes suggest they may be involved in niche adaptation. The authors speculated that the dispensable nature and possession of habitat-determining genes by these chromosomes make them the biological equivalent of bacterial plasmids. It is likely advantageous for a root pathogen to be more competitive in the rhizosphere prior to its entry into the roots of its host.
September 6th, 2009 by Francis Martin
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The latest version of the Integrated Microbial Genomes (IMG) Expert Review (ER) is now available, featuring a baseline of 5,115 isolate genomes from the recently released IMG 2.9.
These genomes together with 148 Genomic Encyclopedia of Bacteria and Archaea (GEBA) genomes (http://www.jgi.doe.gov/sequencing/GEBAseqplans.html) serve as the comparative context for the annotation review and curation of unpublished (so-called “private”) genomes conducted with IMG ER by scientists worldwide.
A paper on IMG ER has recently been published in the journal BIOINFORMATICS. IMG is accessible at http://img.jgi.doe.gov/.
August 28th, 2009 by Francis Martin
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Soil fungi play a major role in ecological and biogeochemical processes in forest ecosystems. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). Within the framework of our metagenomics project aimed to assess the microbial diversity in temperate forests, we surveyed the fungal diversity in six different forest soils at the Breuil-Chenue long-term observatory using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). The paper reporting this study is now online on the New Phytologist Early View pages.
No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units (MOTU). Most MOTUs (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant MOTUs showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp.
This study, together with two other surveys exploring the diversity of fungal communities in Quercus macrocarpa phyllosphere (Jumpponen & Jones, 2009) and the diversity of arbuscular mycorrhiza fungi in a boreonemoral forest (Öpik et al., 2009), validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will likely accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.
Buée et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, doi: 10.1111/j.1469-8137.2009.03003.x
Jumpponen & Jones (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, doi: 10.1111/j.1469-8137.2009.02990.x
Öpik et al. (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, doi: 10.1111/j.1469-8137.2009.02920.x
August 28th, 2009 by Francis Martin
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The Xth International Fungal Biology Conference will be held in Ensenada, Baja California, Mexico on December 6 – 10, 2009. The International Fungal Biology Conferences are a prestigious series of conferences held at 3-4 year intervals at different locations around the world.
Several talks and symposia will be dedicated to genomics and postgenomics of fungi.
Please visit the website for details on the scientific programme, registration, hotel accommodations, transportation etc.
