title: A population genomics insight into the Mediterranean origins of wine yeast domestication.
abstract: The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.
authors.affiliation: UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Almeida
authors.affiliation: UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Barbosa
authors.affiliation: Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000, Ljubljana, Slovenia.
authors.forename: Polona
authors.initials: P
authors.lastname: Zalar
authors.affiliation: Department of Applied Material and Life Science, College of Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama, 236-8501, Japan.
authors.forename: Yumi
authors.initials: Y
authors.lastname: Imanishi
authors.affiliation: Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8673, Japan.
authors.forename: Kiminori
authors.initials: K
authors.lastname: Shimizu
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari e Ambientali & Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia, Borgo XX Giugno, 74 - 06121, Perugia, Italy.
authors.forename: Benedetta
authors.initials: B
authors.lastname: Turchetti
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Legras
authors.affiliation: UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Marta
authors.initials: M
authors.lastname: Serra
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Dequin
authors.affiliation: CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.affiliation: CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Guy
authors.affiliation: Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
authors.forename: Douda
authors.initials: D
authors.lastname: Bensasson
authors.affiliation: UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Paula
authors.initials: P
authors.lastname: Gonçalves
authors.affiliation: UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: José Paulo
authors.initials: JP
authors.lastname: Sampaio
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D016681:Genome, Fungal; D019083:Mediterranean Region; D018895:Microsatellite Repeats; D008957:Models, Genetic; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D029963:Quercus / Q000382:microbiology; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014920:Wine / Q000382:microbiology*
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
keywords: comparative genomics; domestication fingerprints; microbe domestication; microbe population genomics; yeast molecular ecology