Category Archives: yeast

Postdoc: Yeast evolutionary genomics, UW Madison

Chris Hittinger at UW Madison is seeking a highly motivated postdoctoral researcher with an exceptional background in bioinformatics, functional genomics, or evolutionary genomics. Experience analyzing Illumina sequence data, computer programming proficiency, and training in ecological or evolutionary genetics are highly desirable.

The lab has recently received generous funding for yeast
evolutionary genomics research from the National Science
Foundation¢s Dimensions of Biodiversity Program
and the Pew Charitable Trusts

With Antonis Rokas (Vanderbilt) and Cletus P. Kurtzman (USDA), the Y1000+ Project ( seeks to sequence and analyze the to complete genomes of all ~1,000 known species of Saccharomycotina yeasts and determine the genetic basis of their metabolic, ecological, and functional diversification. Yeasts are genetically more diverse than vertebrates and have remarkable metabolic dexterity, but most remain minimally characterized. They compete vigorously for nutrients in every continent and biome and can produce everything from beer to oil. The history of yeasts is recorded in their genome sequences. Now is the time to read it and tell their story!

The Hittinger Lab has diverse funding for other basic and applied research from NSF, DOE, and USDA, but we are specifically expanding our basic research in ecological and evolutionary genomics.

The complete advertisement and application instructions can be found here:

The precise start date is flexible, but candidates should apply by November 30th to receive full consideration.


Chris Todd Hittinger, Assistant Professor of Genetics
Genome Center of Wisconsin
J. F. Crow Institute for the Study of Evolution
University of Wisconsin-Madison
425-G Henry Mall, 2434 Genetics/Biotechnology Center
Madison, WI 53706-1580, (608) 890-2586

Deep EST sequencing = RNA-Seq

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.  

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. (2008). The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science DOI: 10.1126/science.1158441


Yes, Ecology can improve Genomics

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. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.

Continue reading Yes, Ecology can improve Genomics

Yeast genome: Known knowns, and known unknowns

From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast – so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I’ll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown.

I think this sentence from the abstract hits the nail on the head.

Notably,the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory.

Continue reading Yeast genome: Known knowns, and known unknowns

Fungal tree of life papers

Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life project.

Some highlights – there are just too many papers in the issue to cover them all. As usual with more detailed studies of clades with molecular sequences we find that morphologically defined groupings aren’t always truly monophyletic and some species even end up being reclassified. Not that molecular sequence approaches are infallable, but for many fungi the morphological characters are not always stable and can revert (See Hibbet 2004 for a nice treatment of this in mushrooms; subscription required).

  • Meredith Blackwell and others describe the Deep Hypha research coordination network that helped coordinate all the Fungal Tree of Life-rs.
  • John Taylor and Mary Berbee update their previous dating work with new divergence dates for the fungi using as much of the fossil evidence as we have.
  • The early diverging Chytridiomycota, Glomeromycota, and Zygomycota are each described. Tim James and others present updated Chytridiomycota relationships so of which were only briefly introducted in the kingdom-wide analysis paper published last year.
  • There is a nice overview paper of the major Agaricales clades (mushrooms for the non-initiated) from Brandon Matheny as well as as individual treatment of many of the sub-clades like the cantharelloid clade (mmm chanterelles…) .
  • Relationships of the Puccinia clade are also presented – we blogged about the wheat pathogen P. graminis before.
  • A new Saccharomycetales phylogeny is presented by Sung-Oui Suh and others.
  • The validity of the Archiascomycete group is also tested (containing the fission yeast Schizosaccharomyces pombe and the mammalian pathogen Pneumocystis) and they confirm that it is basal to the two sister clades the euascomycete (containing Neurospora) and hemiascomycete (containing Saccharomyces) clades. However it doesn’t appear there are enough sampled species/genes to confirm monophyly of the group. There are/will be soon three genome sequences of Schizosaccharomyces plus one or two Pneumocystis genomes – it will be interesting to see how this story turns out if more species can be identified.

This was a monster effort by a lot of people who it is really nice to see it all have come together in what looks like some really nice papers.

Would a Beetle by another name smell as sweet?

I read this blurb in the New Scientist about a PNAS paper (subscription required for next 6 months) on how hive beetles (Aethina tumida) are able to infest bee hives by throwing off the bees because they are producing isopentyl acetate which is thought to be produced and used by bees to signal an alarm. So the increased levels of the pheromone disorients the bees allowing beetles to continue infecting. European bees appear to be susceptible to this attack while the African bees have apparently evolved to better handle the beetle infestation. I’m not clear if the African bees have a different behavior or if they have different biochemical pathways/receptors to not be fooled by the cheap perfume of the invaders.

Beetles + isopentyl acetate = Unstoppable!

The fungus part here is that the beetles are carrying a hemiascomycete yeast, Kodamaea ohmeri in the Saccharomyces clade (see Suh and Blackwell 2005 for more details), which produces the isopentyl acetate pheromone. So it is a sort of auto-immune hive reaction where the defense mechanism is being short-circuited and harming the host.

Continue reading Would a Beetle by another name smell as sweet?

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.