The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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Deep EST sequencing = RNA-Seq

Posted on May 6th, 2008 by Jason Stajich · No Comments

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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Categories: genome sequencing · saccharomyces · yeast

EMBO workshop on Evolutionary and Environmental Genomics of Yeasts

Posted on April 24th, 2008 by Jason Stajich · No Comments

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

Summer 2008, Mycological Meetings

Posted on April 13th, 2008 by Jason Stajich · No Comments

A few of the summer meetings that relate to fungal biology and evolution. 
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Categories: Mycological Society of America · conferences · news

A lot can happen after a few drinks: Saccharomyces hybridization

Posted on April 9th, 2008 by Jason Stajich · No Comments

ResearchBlogging.org

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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Categories: phylogeny · recombination · saccharomyces

Aspergillus comparative transcriptional profiling

Posted on March 12th, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

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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Categories: aspergillus · evolution · gene regulation · microarray

Some links

Posted on March 3rd, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

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.

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Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete

New Saccharomyces resequencing assembly

Posted on February 21st, 2008 by Jason Stajich · No Comments

SGRP LogoDavid 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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Categories: SGRP · genome · genome sequencing · population genomics · resequencing · saccharomyces

Dandruff genomics

Posted on November 9th, 2007 by Jason Stajich · 2 Comments

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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Categories: basidiomycota · genome · genome annotation · genome sequencing

Yeast resequencing update

Posted on October 16th, 2007 by Jason Stajich · 1 Comment

Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.
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Categories: genome sequencing · news · resequencing · saccharomyces

Yes, Ecology can improve Genomics

Posted on October 5th, 2007 by sharpton · 1 Comment

Blogging on Peer-Reviewed ResearchFew organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
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Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast