The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings. The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons
Podospora genome published
Posted on May 11th, 2008 by Jason Stajich · No Comments
The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings. The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons
Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes
RIPing in an asexual fungus
Posted on March 23rd, 2008 by Jason Stajich · 3 Comments
A paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi. RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae. However, I think this study is the first to describe RIP in a putatively asexual fungus. The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium. A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.
Categories: RIP · aspergillus · fusarium · magnaporthe · neurospora
(re)Annotating GenBank
Posted on March 22nd, 2008 by Jason Stajich · No Comments
There's a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I'm sure he is thinking of many examples, like reclassifying some Drosophila sequence traces.
Categories: database · fungi · metagenomics · news
Aspergillus comparative transcriptional profiling
Posted on March 12th, 2008 by Jason Stajich · 1 Comment
Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.
Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.
Categories: aspergillus · evolution · gene regulation · microarray
B. dendrobatidis strain JAM81 released
Posted on March 6th, 2008 by Jason Stajich · No Comments
The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.
Categories: chytridomycota · genome · news
Phytopathogenic Fungi: what have we learned from genome sequences?
Posted on February 8th, 2008 by Jason Stajich · No Comments
A review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.
Categories: comparative · dothideomycetes · euriotiomycetes · fusarium · magnaporthe · phylogeny · plant pathogen · secondary metabolite
Saccharomyces strain sequencing
Posted on November 20th, 2007 by Jason Stajich · No Comments
"Finally, we made the YJM789 genome a free-to-access resource that marks an initial step toward a more complete set of reference sequences for the S. cerevisiae species"While I am happy to see the sequence resource freely available now, I guess I've come to expect this with any genome publication. The sequence has been available with some restrictions at least since 2003 before the genome was published in a journal. I am unsure why this needs to be championed in the conclusion, shouldn't it be available as a consequence of how it was funded or am I expecting too much?
"This work was supported by National Institutes of Health Grants HG02052 (to R.W.D.), GM068717 (to R.W.D. and L.M.S.), and HG000205 (to R.W.D. and L.M.S.);"There is more discussion of the project and its future at the Stanford site.
Categories: bioinformatics · comparative · human pathogen · resequencing · saccharomyces
Fungal Genetics 2007 details
Posted on March 28th, 2007 by Jason Stajich · 1 Comment
Categories: bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete
Approaching 100% coverage for GO assignments in S.pombe
Posted on March 4th, 2007 by Jason Stajich · 2 Comments
Categories: functional · genome annotation · s.pombe
