An early access to article in Science A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (direct link since DOI is not updated yet) using the current favorite buzzword, metagenomics, of course, describes some early work to try and discover what is killing the honeybees. It is early access and non-free and ScienceExpress is not part of our subscription here so I’ve not actually had a chance to read it yet, but the gist of the reporting about it suggest that a virus is to blame. This is in line with what Joe DeRisi and collaborators found using their Virus chip based on some news reports earlier this year, but no scientific article yet to follow this up.
Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes
- The Dothideomycete leaf streak disease causing fungus Mycosphaerella fijiensis
- Soybean rust Phakopsora pachyrhizi
- The Basidiomycete and jelly fungus Tremella mesenterica proposed by Joe Heitman for use as outgroup to the human pathogen Cryptococcus
- The plant pathogen Cochliobolus heterostrophus proposed by Gillian Turgeon which ironically was already sequenced at the now closed Syngenta Torrey Mesa Research Institute (i.e. this paper on NRPS which used the genome)
- The Sordariale Thielavia terrestris proposed by Novoenzymes presumably for potential in producing novel cellulases as part of biofuel production research.
- The Sordariale and Chestnut blight fungus Cryphonectria parasitica
- EST sequencing for Aspergillus terreus proposed by Scott Baker at PNNL
- Scott is also helping lead a projects to sequence Piromyces and Orpinomyces both early branching Neocallimastigomycota fungi that live in the rumen (which I am probably a little too excited about). Apparently the high A-T content is causing problems in the sequencing phase.
- Agaricus bisporus, sadly the only mushroom some people ever eat (canned and put on pizza or from canned soup), proposed by Mike Challen is also slated to be sequencing in 2008. Did Campell’s already sequence it anyways? We got to see them in their non-native habitat on a field trip in the fall (more pictures!).
- The Basidiomycete EM fungus Paxillus involutus proposed by Anders Tunlid will complement ongoing work in plant-fungal association work.
- Heterobasidion annosu, a basidiomycete fungal pathogen of conifers.
- Three Neurospora genomes proposed by our lab
- The oyster mushroom Pleurotus ostreatus
- The amphibian pathogen Batrachochytrium dendrobatidis that I’m working on with collaborators at Berkeley and the Broad Institute (which sequenced another strain)
- Trichoderma actrovirdi (which doesn’t appear to have any sequence in GenBank) is reportedly in production (bottom of the page).
This complements an ever growing list of fungal genome sequences which is probably topping 80+ now not including the several dozen strains of Saccharomyces that are being sequenced at Sanger Centre and a separately funded NIH project to be sequenced at WashU.
The JGI has released the genome sequence and annotation of the Basidiomycete brown rot Postia placenta. Brown rotters can only break down cellulose but do not degrade lignin that white rotters (like Phanerochaete chrysosporium).
Using total genomic DNA from dikaryotic strain MAD-698, the JGI generated 571,000 reads that assembled into 1243 haplotype scaffolds, with 85 of these scaffolds covering half of the genome sequence.
v.1.0 (September 2006): Postia placenta genome assembly v1.0. The assembly release of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.23X. After trimming for vector and quality, 574,631 reads assembled into 1243 scaffolds totaling 90.9 Mbp.
Since Postia placenta is known to be highly polymorphic with a polymorphism rate in the neighborhood of 3-4%, this particular assembly uses extra stringent parameters that should only assemble sections of the genome that are more than 99% identical.The current draft release, version 1.0, includes a total of 17,173 gene models predicted and functionally annotated using the JGI annotation pipeline.
The genome sequence is a whopping 90 Mb – big for a fungus – but I think this is not just the haploid genome since this was DNA from a dikaryon and only the highly identical haplotypes are assembled together (99% identity). So it means that the haploid genome is not likely to be quite this big. This is much like the Candida albicans diploid assembly. Presumably this means any analysis of gene duplicates needs to have at least two levels of classification to distinguish diploid copy from actual duplicated gene.
While nowhere near the density of sampling of genomes in the Ascomycota, the Basidiomycetes are starting to get their due. Kudos to the JGI for tackling this and the DOE and many of the researchers including Dan Cullen to work to get these genomic resources produced. This genome will be important in work to understand forest ecosystems, process of wood rotting, and maybe even in work to develop better fermentation systems for production of biofuels from cellulose.
We got word last week from the JGI that our DNA for Neurospora tetrasperma and N. discreta have passed QC and library QC and are on their way to being sequenced. The center also plans to do some EST sequencing to improve gene calling abilities.
Why more Neurospora genomes? The sequencing proposal discussed these species as a model system for evolutionary and ecological genetics. It will allow us and others to test several hypotheses about the molecular evolution of things like genome defense in Neurospora and to understand more about the evolutionary history of the model organism N. crassa.
The Saccharomyces Genome Resequencing Project has completed ” ABI sequencing of 32 S. cerevisiae strains and 27 S. paradoxus strains to a depth of between 1x and 3x”. This is in collaboration with Ed Louis’ group who have been working on number of really interesting fungal biology and evolutionary questions. Continue reading Yeast resequencing data updated