A population genomics insight into the Mediterranean origins of wine yeast domestication

被引:130
作者
Almeida, Pedro [1 ]
Barbosa, Raquel [1 ]
Zalar, Polona [2 ]
Imanishi, Yumi [3 ]
Shimizu, Kiminori [4 ]
Turchetti, Benedetta [5 ,6 ]
Legras, Jean-Luc [7 ]
Serra, Marta [1 ]
Dequin, Sylvie [7 ]
Couloux, Arnaud [8 ]
Guy, Julie [8 ]
Bensasson, Douda [9 ]
Goncalves, Paula [1 ]
Sampaio, Jose Paulo [1 ]
机构
[1] Univ Nova Lisboa, Fac Ciencias & Tecnol, Dept Ciencias Vida, UCIBIO REQUIMTE, P-2829516 Caparica, Portugal
[2] Univ Ljubljana, Biotech Fac, Dept Biol, SI-1000 Ljubljana, Slovenia
[3] Kanto Gakuin Univ, Coll Engn, Dept Appl Mat & Life Sci, Kanazawa Ku, Yokohama, Kanagawa 2368501, Japan
[4] Chiba Univ, Med Mycol Res Ctr, Chuo Ku, Chiba 2608673, Japan
[5] Univ Perugia, Dipartimento Sci Agr Alimentari & Ambientali, I-06121 Perugia, Italy
[6] Univ Perugia, Ind Yeasts Collect DBVPG, I-06121 Perugia, Italy
[7] INRA, Sci OEnol SPO UMR1083, F-34060 Montpellier, France
[8] CEA, Inst Genom, Genoscope, Ctr Natl Sequencage, F-91057 Evry, France
[9] Univ Manchester, Fac Life Sci, Manchester M13 9PT, Lancs, England
基金
英国自然环境研究理事会;
关键词
comparative genomics; domestication fingerprints; microbe domestication; microbe population genomics; yeast molecular ecology; SACCHAROMYCES-CEREVISIAE; MAXIMUM-LIKELIHOOD; WILD; DIVERSITY; GENETICS; SEQUENCE; INFERENCE; PARADOXUS; IMPRINT; STRAINS;
D O I
10.1111/mec.13341
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:5412 / 5427
页数:16
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