title: Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation.
abstract: Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains.
authors.affiliation: Department of Bioengineering, School of Food Sciences and Biotechnology, Zhejiang Gongshang University, Hangzhou, China lyd@zjsu.edu.cn jchen@jiangnan.edu.cn zhenguolin@slu.edu.
authors.forename: Yudong
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China.
authors.forename: Weiping
authors.initials: W
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Daoqiong
authors.initials: D
authors.lastname: Zheng
authors.affiliation: College of Life Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Zhan
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Department of Bioengineering, School of Food Sciences and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Yu
authors.affiliation: Department of Bioengineering, School of Food Sciences and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Bioengineering, School of Food Sciences and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Feng
authors.affiliation: Department of Bioengineering, School of Food Sciences and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
authors.forename: Xinle
authors.initials: X
authors.lastname: Liang
authors.affiliation: College of Life Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Guan
authors.affiliation: Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China.
authors.forename: Jingwen
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China lyd@zjsu.edu.cn jchen@jiangnan.edu.cn zhenguolin@slu.edu.
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Biology, Saint Louis University Department of Ecology and Evolutionary Biology, Rice University lyd@zjsu.edu.cn jchen@jiangnan.edu.cn zhenguolin@slu.edu.
authors.forename: Zhenguo
authors.initials: Z
authors.lastname: Lin
mesh_terms: D002681:China; D019143:Evolution, Molecular; D005285:Fermentation; D016681:Genome, Fungal; D023281:Genomics; D012275:Oryza / Q000378:metabolism / Q000382:microbiology*; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014920:Wine / Q000382:microbiology*
chemical_list: D029701:Saccharomyces cerevisiae Proteins
keywords: RNA-Seq; Saccharomyces cerevisiae; evolution; genome; rice wine