Identification of European isolates of the lager yeast parent Saccharomyces eubayanus

Abstract

Lager brewing first occurred in Bavaria in the 15th century, associated with restrictions of brewing to colder months. The lager yeast, Saccharomyces pastorianus, is cold tolerant. It is a hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus, and has been found only in industrial settings. Natural isolates of S. eubayanus were first discovered in Patagonia 11 years ago. They have since been isolated from China, Tibet, New Zealand, and North America, but not from Europe. Here, we describe the first European strains UCD646 and UCD650, isolated from a wooded area on a university campus in Dublin, Ireland. We generated complete chromosome level assemblies of both genomes using long- and short-read sequencing. The UCD isolates belong to the Holarctic clade. Genome analysis shows that isolates similar to the Irish strains contributed to the S. eubayanus component of S. pastorianus, but isolates from Tibet made a larger contribution.

Keywords: European; genome evolution; lager parent; yeast.

Figure 1.

Identification and growth of S. eubayanus isolates. (A) Saccharomyceseubayanus UCD646 and UCD650 were identified in soil from a wooded area on the campus of University College Dublin. One soil sample was isolated from an area with oak, beech, and cherry laurel trees. (B) Isolates were streaked on YPD and incubated at the temperatures shown for 6 days. Sc = S. cerevisiae; Su = S. uvarum (UCD415 was also isolated from soil); and Se = S. eubayanus. CBS 12357 is the S. eubayanus type strain, obtained as VTT-C-72902. Room temperature is approximately 20°C.

Figure 2.

The Irish S. eubayanus isolates belong to the Holarctic clade. Unrooted maximum-likelihood tree of 89 S. eubayanus and two S. pastorianus strains was constructed with RAxML using the GTRGAMMA model of nucleotide substitution, using a concatenated SNP alignment of 319 298 SNP sites. Coloured shapes highlight distinct populations identified previously (Nespolo et al. 2020), and the two Irish (UCD) isolates are highlighted in bold. Most strain labels have been omitted for clarity (see Figure S1, Supporting Information). Branch colour denotes support values on a scale from 0 (red) to 100 (green). All branches in the Holarctic clade have a support value of 100. Support values < 100 are labelled in Figure 1 (Supporting Information).

Figure 3.

Shared ancestry of alleles between the S. eubayanus component of S. pastorianus genomes (CBS 1538 and W34/70) and Holarctic clade S. eubayanus isolates. Coloured offset vertical lines represent sites where an allele in a S. pastorianus strain is also present in only one other population (Tibet = Blue, Ireland = Magenta, or North Carolina = Green) in the Holarctic clade. Coloured rectangles represent blocks assigned to these populations, where blocks contain two or more neighboring alleles from the same population (borders are drawn at half the distance between the outermost sites). All alleles were called by alignment to the UCD646 assembly. Sites where a genotype could not be called or were filtered out are shown in black. All chromosome comparisons are shown in Figure S2 (Supporting Information), and supporting data is in Table S1 (Supporting Information). (A) Shared ancestry blocks of CBS 1538 and W34/70 on Chr XVI. CBS 1538 and W34/70 have similar patterns of ancestry except for a large region marked with a red box where CBS 1538 has shared ancestry with the Tibet population and W34/70 has shared ancestry with the Irish population. In addition, there are large regions in W34/70 where shared ancestry could not be reliably assigned. (B) Shared ancestry blocks of CBS 1538 and W34/70 on Chr XII. This example shows shared ancestry with all three Holarctic populations, although blocks assigned to North Carolina are shorter and fewer in number compared to Irish or Tibet blocks. Again, W34/70 has large blocks where no shared ancestry could be assigned.

Figure 4.

Maltose utilization in S. eubayanus. (A).Organization of maltose utilization genes. Telomeres are indicated with red boxes, and chromosomes with black lines. Maltose utilization genes are shown in colour, and other genes in grey. Intact MAL loci are highlighted with black boxes. Truncated open reading frames are shown as outlines with black asterisks. Ty = Ty element; rDNA = ribosomal DNA locus. Information for S. eubayanus CBS 12357 is from the assembly from Brickwedde et al. (2018) and for CDFM21L.1 is from Brouwers et al. (2019a). (B) Cultures of S. eubayanus CBS 12357, UCD646, and UCD650 and S. cerevisiae S288C were grown at room temperature in YP containing either 2% glucose or 2% maltose as the sole carbon source. Growth was monitored every 10 min. The mean and standard deviation of three biological replicates is shown. (C) Cells from the indicated strains were diluted ⅕ and spotted on YP agar with 2% glucose or 2% maltose and grown at room temperature for 72 h.