Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.
Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP.
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
Brigida
B
Gallone
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Jan
J
Steensels
White Labs, 9495 Candida Street, San Diego, CA 92126, USA.
Troels
T
Prahl
Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA.
Leah
L
Soriaga
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Veerle
V
Saels
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Beatriz
B
Herrera-Malaver
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Adriaan
A
Merlevede
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Miguel
M
Roncoroni
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
Karin
K
Voordeckers
Encinitas Brewing Science, 141 Rodney Avenue, Encinitas, CA 92024, USA.
Loren
L
Miraglia
Illumina, 5200 Illumina Way, San Diego, CA 92122, USA.
Clotilde
C
Teiling
Illumina, 5200 Illumina Way, San Diego, CA 92122, USA.
Brian
B
Steffy
Biological & Popular Culture (BioPop), 2205 Faraday Avenue, Suite E, Carlsbad, CA 92008, USA.
Maryann
M
Taylor
Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA.
Ariel
A
Schwartz
Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA.
Toby
T
Richardson
White Labs, 9495 Candida Street, San Diego, CA 92126, USA.
Christopher
C
White
Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
Guy
G
Baele
Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium. Electronic address: steven.maere@psb.vib-ugent.be.
Steven
S
Maere
Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium. Electronic address: kevin.verstrepen@biw.vib-kuleuven.be.
Kevin J
KJ
Verstrepen
D001515:Beer / Q000382:microbiology*; D056915:DNA Copy Number Variations / Q000235:genetics; D005800:Genes, Fungal / Q000235:genetics; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics; D007218:Industrial Microbiology; D050296:Microbial Viability / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D011003:Ploidies; D012441:Saccharomyces cerevisiae / Q000145:classification* / Q000235:genetics / Q000502:physiology*; D012641:Selection, Genetic