I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers. The data and analyses from these efforts are presented in a publication [...]
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I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus. You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some [...] Take a look at this post by Larry Moran on Takao Kasuga’s paper on phylogenetic distribution of genes in N. crassa genome. [...] The Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the [...] A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the annotation team at Broad’s gene calling pipeline. [...] A new paper in Genome Research from Borodovsky lab at Georgia Tech provides an improved ab initio gene prediction building on their previous program GeneMark called GeneMark.hmm ES. This application doesn’t require a training set when building models for gene prediction in fungal genomes and reports to have as good or better sensitivity and specificity than most of the commonly used ab initio programs. [...] Just noticed that the [[JGI]] has released the Cochliobolus heterostrophus genome sequence at their site predicting 9,633 protein-coding genes. Torrey Mesa Research Institute had access to a sequence many years ago, but it isn’t until now that public version of this genome is available. Cochliobolus is has been a model plant pathogen system and its production of T-Toxin by a PKS gene (Yang et al) [...]
[...] 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 [...]
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The American Academy of Microbiology has 