Some tasty research if you are of the set who enjoy a good pint of beer. GenomeWebNews reports on a study in Genome Research by Barbara Dunn and Gavin Sherlock at Stanford, looking at the history of lager yeast Saccharomyces pastorianus, a hybrid of S. cerevisiae and S. bayanus. Using array Comparative Genome Hybridization (aCGH) they trace the history of S. pastorianus lager strains to show that they sort into two distinct groups indicating there might have been at least two independent origins of the hybrid strain/species both derived from an ale yeast.
The CGH data also indicates there have been many genome rearrangements and aneuploidies after the hybridization providing an interesting picture of recent post-allopolyploidy changes in two independent experiments. Lots more delicious genome evolution details in the paper, so drink up!
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 strains. It seems that the hybrids are better able to cope with the stress associated with fermentation process.
It seems these would also be a great test system for more whole genome sequencing or at least more polymorphism comparisons to try and determine the proportion of the genome that comes from different parents and estimate timing and frequency of hybridization. It seems possible that the hybridizations are occurring multiple times in nature so are the same regions from each parental genome kept in the hybrid offspring that are selected for fitness under fermentation stress?
Gonzalez, S.S., Barrio, E., Querol, A. (2008). Molecular Characterization of New Natural Hybrids of Saccharomyces cerevisiae and S. kudriavzevii in Brewing . Applied and Environmental Microbiology, 74(8), 2314-2320. DOI: 10.1128/AEM.01867-07
In followup to the Aspergillus RIP paper discussion, Jo Anne posted in the comments that her paper published in FGB about RIP in another asexual species of fungi also found that evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).
Continue reading More RIP without sex?
A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and Steinmetz labs to create a high density map of transcription in yeast and for polymorphism mapping from the Kruglyak lab.
Whole genome tiling arrays have also been employed in other fungi. For example, Anita Silâ€™s group at UCSF constructed a random tiling array for Histoplasma capsulatum and used it to identify genes responding to reactive nitrogen species. A similar approach was used in Cryptococcus neoformans to investigate temperature regulated genes using random sequencing clones.
As the technology has become cheaper, it may become sensible to use a tiling array to detect transcripts rather than ESTs when attempting to annotate a genome. In the Histoplasma work transcriptional units could be identified from hybridization alone. Some of the algorithms will need some work to correct incorporate this information, and the sensitivity and density of the array will influence this. These techniques can be part of a resequencing approaches or fast genotyping progeny from QTL experiments when the sequence from both parents is known (or at least enough of the polymorphims for the genetic map).
What is superior about the current Affymetrix yeast tiling array is the inclusion of both strands. This allows detection of transcripts from both strands. Several anti-sense transcripts in yeast have been discovered recently including in the IME4 locus through more classical approaches, but perhaps many more await discovery with high resolution transcriptional data from whole genome tiling arrays.