The Hyphal Tip: Fungal Genomes and Comparative Genomics

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

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

A few of the summer meetings that relate to fungal biology and evolution. 

• Genetics and Cell Biology of Basidiomycetes, May 28-June 1, Southeast Missouri State University, Cape Girardeau, MO. Registration deadline April 25.
• North American Pombe Meeting, June 6-8, Los Angeles, CA. Registration deadline May 14.
• Cellular & Molecular Fungal Biology Gordon Conference, June 29-July 4, The Holderness School, Holderness, NH. Registration deadline June 8 (if it doesn't fill up sooner).
• Yeast Genetics and Molecular

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.

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 sequences".

Steven Salzberg (who is nominated for the Franklin award at bioinformatics.org) has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date. The problem comes down to how annotations are banked. Some people regard GenBank as the gold standard master for annotations, but it only provides a bank.