Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade

Author:

Marr R Alexander12,Moore Jackson12,Formby Sean3,Martiniuk Jonathan T24,Hamilton Jonah2,Ralli Sneha56,Konwar Kishori3,Rajasundaram Nisha3,Hahn Aria3,Measday Vivien2ORCID

Affiliation:

1. Genome Science and Technology Graduate Program, University of British Columbia , Vancouver, BC V5Z 4S6 , Canada

2. Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia , 2205 East Mall, Vancouver, BC V6T 1Z4 , Canada

3. Koonkie Canada Inc. , 321 Water Street Suite 501, Vancouver, BC V6B 1B8 , Canada

4. Food Science Graduate Program, Faculty of Land and Food Systems, University of British Columbia , Vancouver, BC V6T 1Z4 , Canada

5. Canada’s Michael Smith Genome Sciences Centre, BC Cancer , 675 West 10th Avenue, Vancouver, BC V5Z 1L3 , Canada

6. Department of Biomedical Physiology and Kinesiology, Simon Fraser University , 8888 University Drive East K9625, Burnaby, BC V5A 1S6 , Canada

Abstract

Abstract Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The “wine circle/Region B”, a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.

Funder

Investment Agriculture Foundation of BC

Natural Sciences and Engineering Research Council of Canada

Canada Graduate Scholarship—Masters

UBC 4-Year Fellowship

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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