The Hyphal Tip: Fungal Genomes and Comparative Genomics

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

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.

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.

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.

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

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". The authors find a few notable rearrangements and unique genes in this strain as compared to the lab and type strain S288C. They find examples of horizontally transferred genes or potentially genes (like RTM1) which are being exchanged among individuals in the population and just not found in first sequenced strain. There are several other genome architecture observations including numbers of indels and highly polymorphic (and thus different from S288C) ORFs. In general the chromosomes are co-linear but they find some rearrangements. One of the main trains of a human pathogenic fungi, which some people will argue aren't really pathogenic since the host must be severely immunocompromised to infect, is the ability to grow at high or body (37 C) temperatures. Most fungi can't survive at this temperature, but this trait is a necessary condition for fungi like Cryptococcus neoformans, Aspergillus fumigatus, and the pathogenic Candida species like C. albicans to infect and potentially overwhelm a host. Previous work from many of the same authors used a QTL approach to map the high temperature phenotype in a clinical strain Saccharomyces using a new genetic technique called reciprocal-hemizygosity to dissect the QTL. This is only the second actual publication of the genome of another strain of Saccharomyces cerevisiae even though there have been several papers profiling rates of evolution in the lab and wild strains S288C, YJM789, and RM11-1A (Gu 2005, Ronald et al 2006) before the final genome paper was published. I doubt we'll keep seeing papers about a single strain sequenced when there is already a reference strain. Instead papers about clusters of strains or closely related species such nearly complete work in other Saccharomyces strains, Coccidioides and Neurospora will probably be the norm. This paper is available as Open Access through PNAS which I applaud the authors for. However, the paper concludes with a paragraph that starts

"Finally, we made the YJM789 genome a free-to-access resource that marks an initial step toward a more complete set of reference sequences for the S. cerevisiae species"

While I am happy to see the sequence resource freely available now, I guess I've come to expect this with any genome publication. The sequence has been available with some restrictions at least since 2003 before the genome was published in a journal. I am unsure why this needs to be championed in the conclusion, shouldn't it be available as a consequence of how it was funded or am I expecting too much?

"This work was supported by National Institutes of Health Grants HG02052 (to R.W.D.), GM068717 (to R.W.D. and L.M.S.), and HG000205 (to R.W.D. and L.M.S.);"

There is more discussion of the project and its future at the Stanford site.

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.

Reverting CUG tRNA from derived change coding for serine back to leucine (standard code) has profound effect on organism.

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.

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