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.

Keywords: RNA-Seq; Saccharomyces cerevisiae; evolution; genome; rice wine.

Fig. 1.—

Genomic variations of YHJ7 comparing to S288c, K7, and YJSH1. Circle 1: The 16 chromosomes of YHJ7. Circle 2: Density of SNPs (blue) in YHJ7 compared with S288c. The SNP/InDel density was smoothed by a sliding window of the size 2 kb and step size 1 kb to reduce noise. Circle 3: Large deletions (>100 bp, red) in YHJ7 compared with S288c. Circle 4: Density of SNPs (green) in YHJ7 compared with K7. Circle 5: Conserved genomic regions (>200 bp) in YHJ7 compared with three other strains (S288c, K7, and YJSH1). Different conservation levels of genomic regions in YHJ7 are illustrated as different colors explained by the Venn diagram in the center. Specifically, if a genomic region in YHJ7 is only shared with S288c, it is shown in red. Similarly, K7—green; YJSH1—blue. The colors of overlapping circle in the center represent genomic regions in YHJ7 shared with two or three other strains, for example, a genomic region in YHJ7 is shown in purple if it is also found in S288c and YJSH1, and in white if it is conserved among all four strains.

Fig. 2.—

Origin and evolution of YHJ7 strain genes absent in S288c. (A) The YHJ7 g107 gene was likely originated from bacteria by horizontal gene transfer. (B) The homologous sequences of YHJ7 g5169 gene were found in several sake strains as well as other Saccharomyces sensu stricto species, but are absent in many S. cerevisiae strains. The lost of g5169 in S288c is probably due to the highly dynamic activity of subtelomeric region. The evolutionary history was inferred using the NJ method with 1,000 replicates of bootstrap test. The tree is drawn to scale. (C) YHJ7 strain-specific genes located in the subtelomeric regions of chromosomes. The arrows indicate the direction of transcriptions. Genes that are specific to YHJ7 relative to S288c were shaded in red. Genes with orthologous sequences in S288c were shaded in blue. The black dot indicates the end of a chromosome.

Fig. 3.—

Phylogenetic tree of 16 representative strains of S. cerevisiae from various geological locations. The evolutionary history was inferred using the NJ method with 1,000 replicates of bootstrap test based on concatenated nucleotide sequences of 13 phylogenetic informative loci. The tree was drawn to scale. Except for the lab strain S288c, the 15 other S. cerevisiae strains form five well-supported clades. The Huangjiu strain YHJ7 is grouped within the clade of Asian sake strains and is mostly closely related the sake K7 and UC5 strains.