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.
Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse.
But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing). The Aspergillus community now has a AGD – Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation.
I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of people working on related species and willing to work together to coordinate. As these sort of “clade” databases start to develop we will have better clusters of information that can be mapped among multiple species.
Eventually I hope this will spur efforts for more coordinated genome databases for comparative genomic and transfer of known gene and functional information between experimental systems. The efforts really require coordination or centralization of the data so that gene models can be updated as well as orthologs and phylogenomic inference of function.
An avid reader pointed out that I was not entirely thorough in describing that we don’t enough about the V8 agar media that is used to induce mating in Cryptococcus. In fact a great deal of work on mating in this fungus had focused on identifying what pathways are induced by V8 agar that induce mating. It was shown that inositol stimulates mating through use of defined media containing inositol (Xue et al, 2007). This paper interestingly explores plant-fungal interactions and Cryptococcus suggesting that mating may occur preferentially on plants in cases where inositol is abundant.
It is also worth noting that V8 media contains a high level of copper ions and it was also pointed out to me that Jef Edman’s lab showed that melanin mutants have mating defects, and both phenotypes are suppressed by copper. And more recently (Lin et al, PLOS Genetics 2006) found that alleles of the Mac1 copper regulated transcription factor are a QTL influencing hyphal growth and melanin production, and showed that copper can enhance hyphal growth.
So the role of copper and interplay with V8 agar media and how this induces mating is actually quite known.
C XUE, Y TADA, X DONG, J HEITMAN (2007). The Human Fungal Pathogen Cryptococcus Can Complete Its Sexual Cycle during a Pathogenic Association with Plants Cell Host & Microbe, 1 (4), 263-273 DOI: 10.1016/j.chom.2007.05.005