The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

Abstract

Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Σ1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.

Keywords: mapping; next-generation sequencing; phylogeny reconstruction; yeast models.

Figure 1.

Comparing the W303-K6001 genome sequence with whole-genome tiling arrays. The tiling array correctly identified the yeast background, as a significant number of SNV positions were overlapping. However, the tiling array did not reach sensitivity and accuracy of whole-genome resequencing. All unrelated Non-W303 yeast strains share a number of mutant coordinates, indicating errors in the reference genome or tiling array, or private mutations of the S288c line.

Figure 2.

Unequal SNV distribution in the W303 genome illustrates its mutt ancestry. (a) Regions with high-sequence divergence to S288c cluster together. Chromosomal sequences with high identity (less than or equal to 0.5 SNVs per kb) to the S288c Reference genome EF4 are depicted in grey, indicating that 85.4% of the W303-K6001 genome is a S288c descendant. Regions with higher variability form clusters. (b) Median percentage of genetic material with greater than 0.5 SNV per kb divergence from S288c, per chromosome. (c) Distribution of SNV frequencies per 5 kb segment, taking into account all non-S288c clusters larger than 15 kb.

Figure 3.

W303-K6001 contains clusters that are identical to Σ1278B, but differ in S288c. (a) S288c is the main ancestor parent of W303 and Σ1278B; however, part of the non-S288c-derived W303-K6001 genome is also found in Σ1278B. Shown are two exemplary multiple alignments each from Chr. XIV, XIII and XI, and the 3′ breakpoint of the cluster on Chr XI. (b) Distance diagram of S288c, Σ1278B and W303-K6001 for the non-S288c cluster on Chr XIV 730 000–760 000. (c) W303-K6001: non-S288c sequence clusters with high sequence similarity to Σ1278B.