Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research

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 g...

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Main Authors: McIlwain, Sean J., Peris, David, 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
Format: Online
Language:English
Published: Genetics Society of America 2016
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889671/
id pubmed-4889671
recordtype oai_dc
spelling pubmed-48896712016-06-02 Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research McIlwain, Sean J. Peris, David 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 Investigations 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. Genetics Society of America 2016-04-16 /pmc/articles/PMC4889671/ /pubmed/27172212 http://dx.doi.org/10.1534/g3.116.029389 Text en Copyright © 2016 McIlwain et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author McIlwain, Sean J.
Peris, David
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
spellingShingle McIlwain, Sean J.
Peris, David
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
author_facet McIlwain, Sean J.
Peris, David
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
author_sort McIlwain, Sean J.
title Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research
title_short Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research
title_full Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research
title_fullStr Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research
title_full_unstemmed Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research
title_sort genome sequence and analysis of a stress-tolerant, wild-derived strain of saccharomyces cerevisiae used in biofuels research
description 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.
publisher Genetics Society of America
publishDate 2016
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889671/
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