The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.
AAM Releases "The Fungal Kingdom" Report
Posted on July 9th, 2008 by Jason Stajich · 1 Comment
Categories: news · science policy
Theobroma cacao to be sequenced, Oompa Loompa genome to follow.
Posted on June 26th, 2008 by Chris Villalta · 2 Comments
Categories: genome
Basidiomycete genomes galore
Posted on June 1st, 2008 by Jason Stajich · Comments Off
Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles. I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics. I'm happy I got a chance to meet more folks in the community and learned about where informatics is needed
Categories: conferences
Trichoderma reesei genome paper published
Posted on May 12th, 2008 by Jason Stajich · No Comments
The [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.
Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma
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
Deep EST sequencing = RNA-Seq
Posted on May 6th, 2008 by Jason Stajich · No Comments
The transcriptional landscape of yeast has been (further) defined with [[Solexa]] sequencing in a method deemed "RNA-Seq", but what I would call "deep EST sequencing". This approach for transcriptional profiling by sequencing alone is sure to be used by many labs looking for lower and more complete ways to describe and quantitate the full population of transcripts in an organism.
Categories: genome sequencing · saccharomyces · yeast
Rhizoctonia genome project
Posted on April 23rd, 2008 by Jason Stajich · 1 Comment
Jennifer from the other end of the lab just showed me the Rhizoctonia solani genome project page at JCVI. Another Basidiomycete genome on the way, yah!
Categories: basidiomycota · genome sequencing
DuPont donates genome sequence of maize pathogen
Posted on April 3rd, 2008 by Jason Stajich · No Comments
Categories: 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
