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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 involvedmore » 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. Lastly, the Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.« less

Authors:
 [1];  [2];  [3];  [1];  [4];  [5];  [6];  [7];  [1];  [1];  [8];  [9];  [10];  [1];  [11]
  1. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center
  2. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin; Wisconsin Energy Inst., J. F. Crow Institute for the Study of Evolution
  3. Univ. of Wisconsin-Madison, Madison, WI (United States).DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin; Microbiology Doctoral Training Program
  4. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Dept. of Computer Sciences
  5. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin
  6. Univ. of Wisconsin-Madison, Madison, WI (United States). Genome Center of Wisconsin; Dept. of Chemistry
  7. Medical College of Wisconsin, Milwaukee, WI (United States)
  8. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Microbiology Doctoral Training Program; Dept. of Biochemistry
  9. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Genome Center of Wisconsin; Dept. of Chemistry and Biomolecular Chemistry
  10. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin; Microbiology Doctoral Training Program
  11. Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin; Wisconsin Energy Inst., J. F. Crow Institute for the Study of Evolution; Microbiology Doctoral Training Program
Publication Date:
Research Org.:
Univ. of Wisconsin-Madison, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1287334
Grant/Contract Number:  
AC02-05CH11231; FC02-07ER64494
Resource Type:
Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 6; Journal Issue: 6; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; lignocellulosic hydrolysates; Pacific Biosciences (PacBio); genome assembly; genome annotation; novel genes; xylose fermentation; lignocellulosic biomass; gene-transfer; yeast; reveals; dehydrogenase; organization; inhibitors; diversity; evolution

Citation Formats

McIlwain, Sean J., Peris, Davis, Sardi, Maria, Moskvin, Oleg V., Zhan, Fujie, Myers, Kevin S., Riley, Nicholas M., Buzzell, Alyssa, Parreiras, Lucas S., Ong, Irene M., Landick, Robert, Coon, Joshua J., Gasch, Audrey P., Sato, Trey K., and Hittinger, Chris Todd. Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research. United States: N. p., 2016. Web. doi:10.1534/g3.116.029389.
McIlwain, Sean J., Peris, Davis, Sardi, Maria, Moskvin, Oleg V., Zhan, Fujie, Myers, Kevin S., Riley, Nicholas M., Buzzell, Alyssa, Parreiras, Lucas S., Ong, Irene M., Landick, Robert, Coon, Joshua J., Gasch, Audrey P., Sato, Trey K., & Hittinger, Chris Todd. Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research. United States. doi:10.1534/g3.116.029389.
McIlwain, Sean J., Peris, Davis, Sardi, Maria, Moskvin, Oleg V., Zhan, Fujie, Myers, Kevin S., Riley, Nicholas M., Buzzell, Alyssa, Parreiras, Lucas S., Ong, Irene M., Landick, Robert, Coon, Joshua J., Gasch, Audrey P., Sato, Trey K., and Hittinger, Chris Todd. Wed . "Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research". United States. doi:10.1534/g3.116.029389. https://www.osti.gov/servlets/purl/1287334.
@article{osti_1287334,
title = {Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research},
author = {McIlwain, Sean J. and Peris, Davis and Sardi, Maria and Moskvin, Oleg V. and Zhan, Fujie and Myers, Kevin S. and Riley, Nicholas M. and Buzzell, Alyssa and Parreiras, Lucas S. and Ong, Irene M. and Landick, Robert and Coon, Joshua J. and Gasch, Audrey P. and Sato, Trey K. and Hittinger, Chris Todd},
abstractNote = {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. Lastly, the Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.},
doi = {10.1534/g3.116.029389},
journal = {G3},
number = 6,
volume = 6,
place = {United States},
year = {2016},
month = {4}
}

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