The Hyphal Tip

I cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences. They submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published in this instance. The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus.

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Some tasty research if you are of the set who enjoy a good pint of beer. GenomeWebNews reports on study in Genome Research by Barbara Dunn and Gavin Sherlock at Stanford, looking at the history of lager yeast Saccharomyces pastorianus.

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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.

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EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts
taking place at EMBL Heidelberg, 1-5 October 2008

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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

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We may have to reevaluate whether Saccharomyces cerevisiae alone is the species used to brew beer.  A paper from Gonzalez et al describes results from PCR-RFLP comparison of 24 brewing strains identifies evidence for S. cerevisiae x S. kudriavzevii hybrids.  Although this hybridization is not unprecedented, most seem to be related to cultivated brewing or fermentation

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Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

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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.

• FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds – so a database of these enzymes

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David Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 release.

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According to Yahoo News (via GT) , Proctor and Gamble published the genome of the dandruff in PNAS (link not yet available) causing basidiomycete fungus Malassezia globosa. The proteins and genome are available at NCBI.
Update: PNAS paper available.

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