Yeast keeps to itself

Cliff Zeyl and Sally Otto present a nice review on research from the Kruglyak lab regarding evidence that Saccharomyces is primarily a selfer in nature as it outbreeds very infrequently (once in 50,000 generations). The implications of this work has relevance on the importance of sexual reproduction and recombination in natural populations.

Approaching 100% coverage for GO assignments in S.pombe

A paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper on Ashbya annotation database) and doesn’t yet have complete GO coverage. This is quite remarkable and a great dataset for studies in S. pombe and all fungi.

S. pombe taken from Paul Young’s site

My quick predictions of genes a closely related species, S. japonicus, has more than twice as many genes as S. pombe (but be over-prediction by ab initio predictors). Taken in comparison to many other fungi, S. pombe represents a streamlined and reduced genome which probably occured indepdently from reduction in the Hemiascomycetes.

FGI Chytrid annotations available

The public release of the Batrachochytrium dendrobatidis automated annotation from the Broad/FGI has been made available.

“This project is part of the Fungal Genome Initiative at the Broad Institute and was funded by NHGRI. This release contains a set of 8,794 predicted genes, BLAST databases, precomputed BlastX and HMMer analyses, alternative gene predictions, tRNA predictions, and RFAM features.

The annotation can be accessed through the project website:

We would like to thank Franz Lang and Mary Berbee for sharing their B. dendrobatidis EST sequences and contributing a cDNA library for end-sequencing.”

Mystery in the mechanism of yeast speciation

A paper in PLoS Genetics studied what happens when individual chromosomes of S. cerevisiae are replaced with a homologous copy its sister species, S. paradoxus. Previous work from Ken Wolfe’s lab interpreted the differential loss of genes after the whole genome duplication in the Saccharomyces lineage played a role in speciation among the yeast species. Surprisingly (or not, depending on how you interpret the previous work) Greig did not find any lethality in haploid F1 offspring from a diploid synthetically constructed individuals. Certainly this is not the last word but it represents a nice experimental screen to identify interacting genotypes. What would be interesting in followup work would be more subtle dissection of epistatic interactions among the genes on the different chromosomes to score phenotypes other than complete inviability. This might help understand what pathways are operating differently.

Continue reading Mystery in the mechanism of yeast speciation

Fungi for bioremediation

Saprophytic fungi degrade organic matter to release carbon, nitrogen, and other elements locked up in complexes. There is interest in better degradation of recalictrant ligin and cellulose plant matter as part of a bioenergy program. Some fungi are able to break down these plant molecules that would otherwise remain behind when left to digestion by bacteria.

Continue reading Fungi for bioremediation

Full(er) length methods sections in Nature papers

Nature is reporting that it is now going to expand the methods section in print and online versions of its papers. This will also include a 300 word summary of the methods in the print version as well as a full length methods section in the online version which is not a supplemental methods document.

Nature also uses the news piece to remind us that the author formated version of the paper can be submitted to pubmed central (6 months after publication) (well only for NIH supported pubs though – see comments exchange on Jonathan’s blog) and that can include the full length methods.

This seems to be all around a GOOD THING. I’ve always heard complaining about how the glossy publications skimp on actually providing enough evidence to reproduce the results (“telegraphic tradition” in Naturespeak). The best thing is if this means methods are actually peer-reviewed. I don’t really know that they are. You can download the supplemental materials but it isn’t clear to me that someone has actually reviewed it and made sure that a) methods are clearly explained and indicates a reproduceable protocol, b) is typographically proofread.

Wikis for genome (re)annotation

Steven Salzberg (who is nominated for the Franklin award at has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date.
Continue reading Wikis for genome (re)annotation

Evolving a new pathway

A paper* this week from the Huffnagle lab argues that even though the human pathogenic fungus Cryptococcus neoformans can produce an oxylipin similar to prostaglandin, the authors were unable to identify any homologous cyclooxygenase genes in the genome. They showed through LC-MS-MS on supernatants from C. neoformans cells grown on arachidonic acid that molecules with activity similar to prostaglandin E2 are synthesized. BLAST searches of the genome could not identify any similar genes to cyclooxygenase genes including the PPo genes from Aspergillus which contain catalytic domains similar to mammalian cyclooxygenases.

So did C. neoformans evolve a new way to synthesize this enzyme which may act as a hormone and affect the host’s immune system? My cursory searches against other basidiomycete genomes did turn up homologs to these PPo genes in Ustilago and Coprinus so perhaps the enyzmes in the pathway have changed in the Cryptococcus lineage. Perhaps searches with protein structure of cyclooxygenases could pick up functionaly similar genes which would serve as good candidates which have little sequence similarity to the cannonical protein determined in humans.

* Paid access required for 6 months.