The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts

Abstract

The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions.

Keywords: Saccharomyces eubayanus; domestication; genome assembly; hybridization; lager brewing.

Fig. 1.

Dot plot comparing the location of genes in the Saccharomyces eubayanus (FM1318) genome assembly with their location in S. cerevisiae (S288c). Lines circled in the same color indicate reciprocal translocations.

Fig. 2.

Schematic representation of Saccharomyces eubayanus (FM1318) and lager-brewing yeast (Frohberg strain W34/70) annotated mitochondrial genomes. Mitochondrial genes, rRNAs, tRNAs, and noncoding RNAs are represented in green, red, pink, and brown, respectively. Genes with asterisks are elements or gene sequences not shared by both S. eubayanus and the lager yeast mitochondrial genomes. Underlined names are intronic regions located in different positions between S. eubayanus and Frohberg lager yeast.

Fig. 3.

Genome regions in Saccharomyces eubayanus (FM1318) with clusters of genes related to maltose (MAL) utilization. Regions are represented from chromosome ends to the first gene that is syntenic with S. cerevisiae (S288c). Gene sizes and distances are approximately to scale. Arrows show the direction of transcription and direction to the centromeres. Gray boxes represent sequence gaps. MAL genes are colored: Orange genes encode maltases and isomaltases, green genes encode maltose transporters (permeases), and red genes encode transcription factors that regulate other MAL genes. MAL genes are named for their closest S. cerevisiae homolog in S288c and prefixed with “Seub”. S. eubayanus MAL genes that are most similar to the same S. cerevisiae MAL gene are distinguished by letters (SeubIMA-A, SeubIMA-B, etc.). Double lines before or after a gene represent incomplete sequence due to poor sequence resolution in those areas and their names are marked with a “t” for truncated. All non-MAL genes in S. eubayanus are named for their closest gene family in S. cerevisiae using standard names with the exception of genes that are the first gene syntenic with S. cerevisiae (S288c). The first S. eubayanus genes syntenic with S288c are named using the standard names of their S. cerevisiae syntenic homologs, where available, along with their systematic names.

Fig. 4.

Synteny and phylogenetic analysis of MAL genes from Saccharomyces eubayanus (FM1318), S. cerevisiae (S288c), and the Saaz (CBS 1513) and Frohberg (W34/70) lineages of lager-brewing yeasts. Numbers in (A) and (B) indicate genes whose orthology is supported both by synteny and phylogenetic analysis. (A) Solid lines connecting genomes designate blocks of synteny. Chromosome and contig locations are indicated to the left or right of genome segments. The location of the S. cerevisiae segment is indicated by the systematic names of the genes within the syntenic region. Asterisks indicate genes with complete sequences but putatively inactivating mutations. The inactivated Saaz HXT in the region syntenic to S. cerevisiae is divided into two due to an insertion within the gene. Genes are colored as in figure 3. Gene sizes and distances are approximately to scale. Arrows show the directions of transcription. Gray boxes represent gaps in the sequence. Double lines before or after a gene represent incomplete sequence due to poor resolution in those areas, and their names are marked with a “t” for truncated. Dotted lines represent the end of a chromosome or contig. (B) Maximum likelihood trees for maltases, regulators of MAL genes, and maltose permeases (transporters) based on nucleotide sequences. Branch lengths are based on the number of substitutions per site. Bootstrap support values of 70 or higher are shown at nodes. Genes present in the synteny analysis are highlighted by an oval of the same color as their genome blocks in (A). Dashed boxes indicate groups of genes whose ortholog is also supported by synteny. More details on these genes can be found in supplementary table S2, Supplementary Material online.

Fig. 5.

Genome-wide averages of the percent of nonsynonymous substitutions out of all substitutions per gene for the genomes of Saccharomyces cerevisiae, S. eubayanus, and the S. cerevisiae and S. eubayanus subgenomes of lager-brewing yeast hybrids when using either the Frohberg (gray) or Saaz (white) lineage as the representative of lager-brewing yeasts. Substitutions were estimated by PAML phylogenetic analysis using orthologs from S. cerevisiae, S. paradoxus, S. eubayanus, and S. uvarum and orthologs that are present in both the S. cerevisiae and S. eubayanus subgenomes of the Saaz and Frohberg lineages. Only the 2,194 genes shared by both 1:1:1:1:1:1 ortholog sets were included in the analyses. Error bars represent 99% binomial confidence intervals. Comparisons between genomes and subgenomes (and between using Saaz versus Frohberg as the lager yeast representative) were made using logistic regression. Asterisks represent statistically significant comparisons. Note that the enrichment of nonsynonymous changes in lager lineages of S. eubayanus is not due to the inverse correlation between ω and d_S: The average d_S for each branch left to right is 0.0045, 0.0046, 0.0061, 0.0062, 0.0046, 0.0050, 0.0046, and 0.0047; the average d_N for each branch is 0.0006, 0.0006, 0.0017, 0.0019, 0.0010, 0.0013, 0.0010, and 0.0010.

Fig. 6.

(A) Hypothetical models for the origin of hybrid lager-brewing yeast lineages and the relative neutral divergence (d_S and S × d_S) between the subgenomes of each lineage under each model. (B) and (C) are the distributions of the estimated synonymous rates of evolution (d_S) and the estimated number, respectively of synonymous substitutions (S × d_S) for all genes and ten gene windows respectively, between either the Saccharomyces cerevisiae subgenomes (yellow) or the S. eubayanus subgenomes (blue) of the two lager-brewing yeast lineages. Line drawings within graphs represent outlines of the histograms to better show their overall distributions.