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
A lot can happen after a few drinks: Saccharomyces hybridization
Posted on April 9th, 2008 by Jason Stajich · No Comments
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
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
Neurospora speciation through experimental evolution
Posted on February 5th, 2008 by Jason Stajich · No Comments
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.
Categories: adaptation · experimental evolution · neurospora · speciation
Tags: antagonistic epistasis, asexual, biology, cerevisiae, evolution, experimental, filamentous, fitness, fungal, fungi, fungus, hybrid, neurospora, phenotype, phylogenetics, saccharomyces, sequencing, speciation, species, strain
More updates on Saccharomyces resequencing project at Sanger
Posted on December 19th, 2007 by Jason Stajich · 1 Comment
I’ve paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project.
The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite
Categories: population genomics · resequencing · saccharomyces
Tags: cerevisiae, genome sequencing, paradoxus, population genomics, resequencing, saccharomyces
Saccharomyces strain sequencing
Posted on November 20th, 2007 by Jason Stajich · No Comments
While many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789″.
Categories: bioinformatics · comparative · human pathogen · resequencing · saccharomyces
Tags: candida species, comparative, genes, genome, immunocompromised, mushroom, phenotype, qtl, s, saccharomyces, saccharomyces cerevisiae, sequencing, systematics
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.
Categories: genome sequencing · news · resequencing · saccharomyces
Tags: population genomics, resequencing, saccharomyces, SNP, yeast
Exploring CUG codon evolution in Candida
Posted on October 9th, 2007 by Jason Stajich · 1 Comment
Reverting CUG tRNA from derived change coding for serine back to leucine (standard code) has profound effect on organism.
Categories: candida · evolution · fungi · gene regulation · genetic code
Tags: ancestral, candida, character evolution, comparative, genome, leucine, mushroom, pathogen, pathogens, reconstruction, saccharomyces, systematics, tRNA
Yes, Ecology can improve Genomics
Posted on October 5th, 2007 by sharpton · 1 Comment
Few 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.
Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast
Tags: bioinformatics, comparative, functional, gene function, gene knockout, genome, genome annotation, genome sequencing, molecular evolution, saccharomyces, yeast
Genomes on the horizon at JGI
Posted on July 4th, 2007 by Jason Stajich · 1 Comment
Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes
- The Dothideomycete leaf streak disease causing fungus Mycosphaerella fijiensis
- Soybean rust Phakopsora pachyrhizi
- The Basidiomycete and jelly fungus Tremella mesenterica proposed by Joe Heitman for use as outgroup to the human pathogen Cryptococcus
- The plant pathogen Cochliobolus heterostrophus proposed by Gillian Turgeon which ironically was already sequenced
Categories: NRPS · aspergillus · basidiomycota · chytridomycota · cryptococcus · dothideomycetes · fungi · genome · genome sequencing · neurospora · pathogens · plant pathogen · rumen · rusts · saccharomyces
Tags: aspergillus, basidiomycota, chytridomycota, cryptococcus, dothideomycetes, fungi, genome, genome sequencing, neurospora, NRPS, pathogens, plant pathogen, rumen, rusts, saccharomyces
