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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.
Yeast population genomics
Posted on March 1st, 2009 by Jason Stajich · No Comments
Categories: SGRP · bioinformatics · comparative · genome annotation · population genomics · resequencing · saccharomyces · short-read
Tags: fungi, methods, population genomics, resequencing, sequencing, yeast
A brief history of lager yeast
Posted on September 11th, 2008 by Jason Stajich · No Comments
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.
Categories: saccharomyces
Tags: aCGH, beer, CGH, fungi, genome, hybridization, yeast
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.
Categories: genome sequencing · saccharomyces · yeast
Tags: sequencing, solexa, transcripts, 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
Categories: conferences & courses
Tags: EMBO, fungi, workshop, yeast
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.
- 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
Categories: Mycological Society of America · conferences & courses · news
Tags: biology, conferences & courses, fungal, meetings, mycological, yeast
A lot can happen after a few drinks: Saccharomyces hybridization
Posted on April 9th, 2008 by Jason Stajich · No Comments
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
Categories: phylogeny · recombination · saccharomyces
Tags: brewing, fermentation process, fitness, hybrid, hybrid offspring, hybridization, natural hybrids, parents, polymorphism, saccharomyces, saccharomyces cerevisiae, strain, stress, yeast
Aspergillus comparative transcriptional profiling
Posted on March 12th, 2008 by Jason Stajich · 1 Comment
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.
Categories: aspergillus · evolution · gene regulation · microarray
Tags: aspergillus, candida, cerevisiae, comparative, development, evolution, fermentation, filamentous, fungi, gene, genes, genome, microarray, saccharomyces, sequencing, solexa, transcription, yeast
Some links
Posted on March 3rd, 2008 by Jason Stajich · 2 Comments
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.
Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete
Tags: ancestor, ancestral, brown rot, comparative, cryptococcus, database, enzymes, evolution, extremophiles, functional, fungi, fungus, genome, lignin, news, oxidoreductases, phylogenetics, reconstruction, rhizopus, taxa, toxin, white rot, yeast
New Saccharomyces resequencing assembly
Posted on February 21st, 2008 by Jason Stajich · No Comments
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.
Categories: SGRP · genome · genome sequencing · population genomics · resequencing · saccharomyces
Tags: alignment, cerevisiae, genome, maps, news, paradoxus, recombination, resequencing, saccharomyces, sequencing, SGRP, SNP, solexa, yeast
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.
Categories: basidiomycota · genome · genome annotation · genome sequencing
Tags: dandruff, fungi, genome, yeast
