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UW-Madison Study Dips Into Evolutionary History of Lager Yeast

NEW YORK (GenomeWeb) – The yeast used to brew lager beer has long been known to be a hybrid, but until 2011, scientists only knew the identity of one parent, Saccharomyces cerevisiae, which is also used to brew ales, make bread, and synthesize insulin, among other uses.

A few years ago, researchers identified yeast in South America that fit the profile of the lager yeast's missing subgenome, from S. eubayanus. Now, a new study presenting a mostly complete genome assembly for S. eubayanus suggests that the two yeast strains have had an interesting history.

"Lager yeasts did not just originate once," Chris Hittinger, a senior author of the paper in Molecular Biology and Evolution and a professor at the University of Wisconsin-Madison, said in a statement. "This unlikely marriage between two species, genetically as different from one another as humans and birds, happened at least twice. Although these hybrids were different from the start, they also changed in some predictable ways during their domestication."

Lager beer originated in Europe in the 15th century and differs from ale in several ways. The yeast used to make them can grow at lower temperatures and create a crisp flavor profile, among other differences. Lagers, which also include snappy pilsners and dark dunkels, now make up 94 percent of the international beer market.

Led by Hittinger and Emily Clare Baker, also of UW-Madison, the scientists used Illumina next-generation sequencing technology to sequence and assemble the S. eubayanus genome. In the paper, they wrote that they set "a new benchmark for genome assembly quality," creating a genome that exceeds every other Saccharomyces species (aside from S. cerevisiae) in both depth and completeness.

The assembled mitochondrial and nuclear genomes allowed the authors to make several observations, including their proclamation that the two great lineages of lager yeasts had independent origins.

"The multiple origin hypothesis predicts that the parental genomes could have already begun to diverge from each other before hybridizing, leading to potentially different levels of neutral divergence," the authors wrote. Based on the rate of synonymous substitutions in the S. cerevisiae subgenome, compared to that in the S. eubayanus subgenome, they suggested that the two lager yeast lineages were created by hybridizations between genomically similar strains of S. eubayanus, with two more diverse strains of S. cerevisiae.

The study also identified 11 new genes essential for fermentation and brewing related to maltose utilization in S. eubayanus and were able to place them on four chromosomes in the genome. The previous assembly only identified three and couldn't place any on chromosomes.  

The authors said their study was important to help understand the molecular evolutionary processes of domestication and could provide a roadmap for future research. While these processes have been long-studied in plants and animals, they had not been explored in fungi, like yeast. Now, the genome sequence of S. eubayanus can fill in an information gap to help resolve the evolutionary history of lager yeast.