Archive for September, 2009

Sequencing a tree-killing fungus by 454 and Illumina

September 29th, 2009

ponderosae

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

Genome Of Irish Potato Famine Pathogen Decoded

September 20th, 2009

cover_nature

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.

Supernumerary chromosomes in a root-rot fungus

September 20th, 2009

lascaux_horseFungal 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.

Latest version of the Integrated Microbial Genomes Expert Review is online

September 6th, 2009

img2The 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 BIOINFORMATICSIMG is accessible at http://img.jgi.doe.gov/.