By Jason Stajich, on May 26th, 2009
Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news. Here’s a short list of links and papers that are worth a look though.
“Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
NYT Science article sort of summarizing the good, bad, and ugly of fungi [...]
By Jason Stajich, on April 22nd, 2009
By Jason Stajich, on February 9th, 2009
The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work. These are two closely related species to the well studied laboratory workhorse Neurospora crassa.
The N.tetrasperma assembly (8X) has an N50 of 976kb and is [...]
By Jason Stajich, on June 16th, 2008
This is a research blog so I though I’d post some quick numbers we are seeing for de novo assembly of the [[Neurospora crassa]] genome using Velvet. The genome of N.crassa is about 40Mb and sequencing of several flow cells using Solexa/Illumina technology to see what kind of de novo reconstruction we’d get. [...]
By Jason Stajich, on May 11th, 2008
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 [...]
By Jason Stajich, on April 5th, 2008
Another asexual species of fungi also has evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP). [...]
By Jason Stajich, on March 23rd, 2008
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. [...]
By Jason Stajich, on February 5th, 2008
Dettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.
By Jason Stajich, on September 21st, 2007
By Jason Stajich, on July 4th, 2007
Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes
A quick link to a Neurospora paper in Genetics today entitled