Tag Archives: genome sequencing

Genomes on the horizon at JGI

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes

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.

Genome of Postia placenta

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.

More Neurospora genomes

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.

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