Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of saccharomyces cerevisiae

Anthony R. Borneman, Brian A. Desany, David Riches, Jason P. Affourtit, Angus H. Forgan, Isak S. Pretorius, Michael Egholm, Paul J. Chambers

Research output: Contribution to journalArticleResearchpeer-review

Abstract

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.

LanguageEnglish
Article numbere1001287
Pages1-10
Number of pages10
JournalPLoS Genetics
Volume7
Issue number2
DOIs
Publication statusPublished - 7 Feb 2011
Externally publishedYes

Fingerprint

Saccharomyces cerevisiae
genome
Genome
genome assembly
yeast
Open Reading Frames
open reading frames
Yeasts
Wine
brewing
yeasts
wines
domestication
Circular DNA
circular DNA
bioethanol
genetic variation
artificial selection
comparison
industrial applications

Bibliographical note

Copyright the Author(s) [2011]. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Cite this

Borneman, Anthony R. ; Desany, Brian A. ; Riches, David ; Affourtit, Jason P. ; Forgan, Angus H. ; Pretorius, Isak S. ; Egholm, Michael ; Chambers, Paul J. / Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of saccharomyces cerevisiae. In: PLoS Genetics. 2011 ; Vol. 7, No. 2. pp. 1-10.
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Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of saccharomyces cerevisiae. / Borneman, Anthony R.; Desany, Brian A.; Riches, David; Affourtit, Jason P.; Forgan, Angus H.; Pretorius, Isak S.; Egholm, Michael; Chambers, Paul J.

In: PLoS Genetics, Vol. 7, No. 2, e1001287, 07.02.2011, p. 1-10.

Research output: Contribution to journalArticleResearchpeer-review

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