The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts.
The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions.
Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison.
EmilyClare
E
Baker
Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison.
Bing
B
Wang
Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina.
Nicolas
N
Bellora
Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison.
David
D
Peris
Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison.
Amanda Beth
AB
Hulfachor
Biotechnology Center, University of Wisconsin-Madison.
Justin A
JA
Koshalek
Biotechnology Center, University of Wisconsin-Madison.
Marie
M
Adams
Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina.
Diego
D
Libkind
Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison cthittinger@wisc.edu.
Chris Todd
CT
Hittinger
D001483:Base Sequence; D001515:Beer / Q000382:microbiology; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D016681:Genome, Fungal; D023281:Genomics; D006824:Hybridization, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012440:Saccharomyces / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics
Saccharomyces eubayanus; domestication; genome assembly; hybridization; lager brewing