Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7

Abstract

The term 'sake yeast' is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast.

Figure 1.

Dot-plot alignments of homologous chromosomes of S. cerevisiae strains K7 and S288C. The nucleotide sequence of each K7 supercontig was compared with that of the homologous S288C chromosome (indicated above each alignment) using MUMmer 3.0.

Figure 2.

Genome-wide distribution of heterozygosity between homologous chromosomes of K7. Heterozygous sites were identified by manually checking sequence reads assembled within the supercontigs. The frequency of the extracted heterozygosity in homologous K7 chromosomes was plotted by each 10 kb window of the chromosomal coordinates. x-axis, chromosomal corrdinates; y-axis, heterozygosity counts; arrow heads, position of centromeres.

Figure 3.

Identities of K7 ORFs with the top-hit S288C ORF. Each K7 ORF was compared with the corresponding orthologous S288C ORF using BLASTN (nucleotide level) and BLASTP (amino acid level). The ORF proportion based on the observed identities was then plotted.

Figure 4.

Loss of genomic regions by Ty2 replacement in the K7 genome. Each region within the dotted-line box in the S288C genome was replaced by a Ty element (Ty2) in the K7 genome. (A) A 2628-bp region containing the tRNA gene tR(UCU)G3 and PPT1/YGR123C in S288C chromosome VII was replaced by K7_YGRCTy2-2 in K7 chromosome VII. (B) A 2464-bp region containing two tRNA genes, tL(CAA)A and tS(AGA)A, in S288C chromosome I was replaced by K7_YARWTy2-1 in K7 chromosome I.

Figure 5.

Phylogenetic tree of hexose transporter family proteins identified in S288C. The amino acid sequences of S288C HXT gene products were clustered by CLUSTALW 1.83, and the dendrogram was plotted using the TreeView program. Symbols at the end of the branches indicate the structural class of K7 orthologous gene products, as shown in the box under the dendrogram. Two groups of Hxts, whose functional structures were disrupted in K7, are framed with rectangles. Underlines indicate genes whose expression is repressed under high-glucose conditions. The letter (a) denotes each of the two K7 orthologs is indicated as a half round.