title: Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research.
abstract: The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Sean J
authors.identifier: 0000-0002-3820-8400
authors.initials: SJ
authors.lastname: McIlwain
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: David
authors.initials: D
authors.lastname: Peris
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Microbiology Doctoral Training Program, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Maria
authors.initials: M
authors.lastname: Sardi
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Moskvin
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Department of Computer Sciences, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Fujie
authors.initials: F
authors.lastname: Zhan
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Myers
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Riley
authors.affiliation: Medical College of Wisconsin, Milwaukee, Wisconsin 53226.
authors.forename: Alyssa
authors.initials: A
authors.lastname: Buzzell
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Lucas S
authors.initials: LS
authors.lastname: Parreiras
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Irene M
authors.initials: IM
authors.lastname: Ong
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Microbiology Doctoral Training Program, University of Wisconsin-Madison, Wisconsin 53706 Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706 Department of Biomolecular Chemistry, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Microbiology Doctoral Training Program, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Audrey P
authors.initials: AP
authors.lastname: Gasch
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Trey K
authors.initials: TK
authors.lastname: Sato
authors.affiliation: Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53706 Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706 Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706 Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706 Microbiology Doctoral Training Program, University of Wisconsin-Madison, Wisconsin 53706 cthittinger@wisc.edu.
authors.forename: Chris Todd
authors.initials: CT
authors.lastname: Hittinger
mesh_terms: D000220:Adaptation, Biological; D056804:Biofuels; D002244:Carbon / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012106:Research; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D013312:Stress, Physiological
chemical_list: D056804:Biofuels; D002244:Carbon
keywords: Pacific Biosciences (PacBio); genome annotation; genome assembly; lignocellulosic hydrolysates; novel genes