Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

et al. (2011) Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae. PLoS Genet 7(2): e1001287. doi:10.1371/journal.pgen.1001287 Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae Anthony R. Borneman 0 Brian A. Desany 0 David Riches 0 Jason P. Affourtit 0 Angus H. Forgan 0 Isak S. 0 Pretorius 0 Michael Egholm 0 Paul J. Chambers 0 Gavin Sherlock, Stanford University, United States of America 0 1 The Australian Wine Research Institute , Adelaide , Australia , 2 454 Life Sciences, A Roche Company , Branford, Connecticut , United States of America Human intervention has subjected the yeast Saccharomyces cerevisiae to multiple rounds of independent domestication and thousands of generations of artificial selection. As a result, this species comprises a genetically diverse collection of natural isolates as well as domesticated strains that are used in specific industrial applications. However the scope of genetic diversity that was captured during the domesticated evolution of the industrial representatives of this important organism remains to be determined. To begin to address this, we have produced whole-genome assemblies of six commercial strains of S. cerevisiae (four wine and two brewing strains). These represent the first genome assemblies produced from S. cerevisiae strains in their industrially-used forms and the first high-quality assemblies for S. cerevisiae strains used in brewing. By comparing these sequences to six existing high-coverage S. cerevisiae genome assemblies, clear signatures were found that defined each industrial class of yeast. This genetic variation was comprised of both single nucleotide polymorphisms and large-scale insertions and deletions, with the latter often being associated with ORF heterogeneity between strains. This included the discovery of more than twenty probable genes that had not been identified previously in the S. cerevisiae genome. Comparison of this large number of S. cerevisiae strains also enabled the characterization of a cluster of five ORFs that have integrated into the genomes of the wine and bioethanol strains on multiple occasions and at diverse genomic locations via what appears to involve the resolution of a circular DNA intermediate. This work suggests that, despite the scrutiny that has been directed at the yeast genome, there remains a significant reservoir of ORFs and novel modes of genetic transmission that may have significant phenotypic impact in this important model and industrial species. - Funding: The AWRI, a member of the Wine Innovation Cluster in Adelaide, is supported by Australian grapegrowers and winemakers through their investment body, the Grape and Wine Research Development Corporation, with matching funds from the Australian Government. Systems Biology research at the AWRI is performed using resources provided as part of the National Collaborative Research Infrastructure Strategy, an initiative of the Australian Government, in addition to funds from the South Australian State Government. The funders of this work had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: BAD, DR, JPA, and ME were employees of 454 Life Sciences, A Roche Company, at the time this work was performed. During its long history of association with human activity, the genomic makeup of the yeast S. cerevisiae is thought to have been shaped through the action of multiple independent rounds of wild yeast domestication combined with thousands of generations of artificial selection. As the evolutionary constraints that were applied to the S. cerevisiae genome during these domestication events were ultimately dependent on the desired function of the yeast (e.g baking, brewing, wine or bioethanol production), these multitude of selective schemes have produced large numbers of S. cerevisiae strains, with highly specialized phenotypes that suit specific applications [1,2]. As a result, the study of industrial strains of S. cerevisiae provides an excellent model of how reproductive isolation and divergent selective pressures can shape the genomic content of a species. Despite their diverse roles, industrial yeast strains all share the general ability to grow and function under the concerted influences of a multitude of environmental stressors, which include low pH, poor nutrient availability, high ethanol concentrations and fluctuating temperatures. In comparison, non-industrial isolates such as laboratory strains, have been selected for rapid and consistent growth in nutrient rich laboratory media, thereby producing markedly different phenotypic outcomes when compared to their industrial relatives [3]. The outcomes of these very different selection pressures are therefore most evident when comparing industrial and non-industrial yeasts. As an example, laboratory strains of S. cerevisiae, such as S288c, are unable to grow in the low pH and high osmolarity of most grape juices and therefore cannot be used to make wine. This is a clear difference between industrial and non-industrial strains of S. cerevisiae, however there are numerous subtle differences not only between industrial strains, but also between strains used within the same industry [4,5], highlighting the overall genetic diversity found in this species. The yeast S. cerevisiae has been associated with human activity for thousands of years in industries such as baking, brewing, and winemaking. During this time, humans have effectively domesticated this microorganism, with different industries selecting for specific desirable phenotypic traits. This has resulted in the species S. cerevisiae comprising a genetically diverse collection of individual strains that are often suited to very specific roles (e.g. wine strains produce wine but not beer and vice versa). In order to understand the genetic differences that underpin these diverse industrial characteristics, we have sequenced the genomes of six industrial strains of S. cerevisiae that comprise four strains used in commercial wine production and two strains used in beer brewing. By comparing these genome sequences to existing S. cerevisiae genome sequences from laboratory, pathogenic, bioethanol, and natural isolates, we were able to identify numerous genetic differences among these strains including the presence of novel open reading frames and genomic rearrangements, which may provide the basis for the phenotypic differences observed among these strains. There have been several attempts to characterize the genomes of industrial strains of S. cerevisiae which have uncovered differences that included single nucleotide polymorphisms (SNPs), strain-specific ORFs and localized variations in genomic copy number [614]. However, the type and scope of genomic variation documented (...truncated)