By Jason Stajich, on September 14th, 2009
A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation [...]
By Jason Stajich, on March 12th, 2009
The Mucormycotina (formerly Zygomycota) fungus Mucor circinelloides Genome Portal is now publicly available at http://genome.jgi-psf.org/Mucci1/Mucci1.home.html.
If you are planning to attend the Fungal Conference in Asilomar, there will be a JGI Workshop on March 19, 2009 at noon in Chapel to show how to use the manual curation tools.
By Jason Stajich, on September 16th, 2008
In a paper appearing today in PLoS One, “The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi” Nicholas Money and colleagues including 6 undergraduates and 3 graduate students, have measured the speed of flight of spores discharging from several Ascomycete and Zygomycete dung [...]
By Jason Stajich, on August 24th, 2008
A quick post of some recent comparative genomics papers on our desk that are worth a look.
Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal [...]
By Chris Villalta, on May 29th, 2008
I found the headline today, “Biofuels: Fungus Use Improves Corn-to-ethanol Process” and I was curious to find out what fungus they were talking about in the article. It turns out that researchers at Iowa State University found that Rhizopus microsporus is able to grow off part of the leftovers of ethanol production called thin stillage. [...]
By Jason Stajich, on March 3rd, 2008

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.
By Jason Stajich, on January 13th, 2008
On the cover of this week’s Nature is a picture of Phycomyces blakesleeanus
highlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern [...]
By Jason Stajich, on October 16th, 2007
I recently heard through the grapevine that the Mucor ircinelloides genome 4X assembly was completed by JGI and a BLAST server is available if you contact the authors. Mucorales (previously Zygomycota which is not monophyletic) includes previously sequenced Rhizopus oryzae and Phycomyces blakesleeanus which we’ve blogged about before.
Mucor is model system for the Zygos/Mucorales as it can be
By Jason Stajich, on May 15th, 2007
Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life [...]
By Jason Stajich, on March 28th, 2007
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome [...]