Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

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

doi:10.1534/g3.116.029389

Title: Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

Journal Article · Wed Apr 20 00:00:00 EDT 2016 · G3

DOI:https://doi.org/10.1534/g3.116.029389· OSTI ID:1287334

McIlwain, Sean J. ^[1]; Peris, Davis ^[2]; Sardi, Maria ^[3]; Moskvin, Oleg V. ^[1]; Zhan, Fujie ^[4]; Myers, Kevin S. ^[5]; Riley, Nicholas M. ^[6]; Buzzell, Alyssa ^[7]; Parreiras, Lucas S. ^[1]; Ong, Irene M. ^[1]; Landick, Robert ^[8]; Coon, Joshua J. ^[9]; Gasch, Audrey P. ^[10]; Sato, Trey K. ^[1]; Hittinger, Chris Todd ^[11]

Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center
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
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
Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Dept. of Computer Sciences
Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Laboratory of Genetics; Genome Center of Wisconsin
Univ. of Wisconsin-Madison, Madison, WI (United States). Genome Center of Wisconsin; Dept. of Chemistry
Medical College of Wisconsin, Milwaukee, WI (United States)
Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Microbiology Doctoral Training Program; Dept. of Biochemistry
Univ. of Wisconsin-Madison, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; Genome Center of Wisconsin; Dept. of Chemistry and Biomolecular Chemistry
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
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

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; FC02-07ER64494

OSTI ID:: 1287334

Journal Information:: G3, Vol. 6, Issue 6; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 33 works

Citation information provided by
Web of Science

References (78)

Advanced biofuel production by the yeast Saccharomyces cerevisiae Buijs, Nicolaas A.; Siewers, Verena; Nielsen, Jens Current Opinion in Chemical Biology, Vol. 17, Issue 3 https://doi.org/10.1016/j.cbpa.2013.03.036	journal	June 2013
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Auwera, Geraldine A.; Carneiro, Mauricio O.; Hartl, Christopher Current Protocols in Bioinformatics, Vol. 43, Issue 1 https://doi.org/10.1002/0471250953.bi1110s43	journal	October 2013
The UCSC genome browser and associated tools Kuhn, R. M.; Haussler, D.; Kent, W. J. Briefings in Bioinformatics, Vol. 14, Issue 2 https://doi.org/10.1093/bib/bbs038	journal	August 2012
Lignocellulosic Biomass Pretreatment Using AFEX Balan, Venkatesh; Bals, Bryan; Chundawat, Shishir P. S. Biofuels, p. 61-77 https://doi.org/10.1007/978-1-60761-214-8_5	book	January 2009
GenePalette: a universal software tool for genome sequence visualization and analysis Rebeiz, Mark; Posakony, James W. Developmental Biology, Vol. 271, Issue 2 https://doi.org/10.1016/j.ydbio.2004.04.011	journal	July 2004
RACER: Rapid and accurate correction of errors in reads Ilie, Lucian; Molnar, Michael Bioinformatics, Vol. 29, Issue 19 https://doi.org/10.1093/bioinformatics/btt407	journal	July 2013
Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae Wenger, Jared W.; Schwartz, Katja; Sherlock, Gavin PLoS Genetics, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pgen.1000942	journal	May 2010
The One Hour Yeast Proteome Hebert, Alexander S.; Richards, Alicia L.; Bailey, Derek J. Molecular & Cellular Proteomics, Vol. 13, Issue 1 https://doi.org/10.1074/mcp.M113.034769	journal	October 2013
Cloning and sequence determination of the gene encoding sorbitol dehydrogenase from Saccharomyces cerevisiae Sarthy, Aparna V.; Schopp, Cynthia; Idler, Kenneth B. Gene, Vol. 140, Issue 1 https://doi.org/10.1016/0378-1119(94)90741-2	journal	January 1994
Characterization of the Saccharomyces cerevisiae YMR318C (ADH6) gene product as a broad specificity NADPH-dependent alcohol dehydrogenase: relevance in aldehyde reduction Larroy, Carol; Fernandez, M. Rosario; Gonzalez, Eva Biochemical Journal, Vol. 361, Issue 1, p. 163-172 https://doi.org/10.1042/bj3610163	journal	January 2002
Draft Genome Sequence of Saccharomyces cerevisiae IR-2, a Useful Industrial Strain for Highly Efficient Production of Bioethanol Sahara, T.; Fujimori, K. E.; Nezuo, M. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomeA.01160-13	journal	January 2014
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
Saccharomyces diversity and evolution: a budding model genus Hittinger, Chris Todd Trends in Genetics, Vol. 29, Issue 5 https://doi.org/10.1016/j.tig.2013.01.002	journal	May 2013
Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production Wohlbach, Dana J.; Rovinskiy, Nikolay; Lewis, Jeffrey A. Genome Biology and Evolution, Vol. 6, Issue 9 https://doi.org/10.1093/gbe/evu199	journal	September 2014
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production G. S., Andrietta, M.; A. G., Pereira, G.; O., Vidal, R. The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/2dgm-6222	text	January 2009
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries Hong, Kuk-Ki; Nielsen, Jens Cellular and Molecular Life Sciences, Vol. 69, Issue 16 https://doi.org/10.1007/s00018-012-0945-1	journal	March 2012
Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1 Babrzadeh, Farbod; Jalili, Roxana; Wang, Chunlin Molecular Genetics and Genomics, Vol. 287, Issue 6 https://doi.org/10.1007/s00438-012-0695-7	journal	May 2012
AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae Song, Giltae; Dickins, Benjamin J. A.; Demeter, Janos PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0120671	journal	March 2015
Whole-Genome Sequencing of Sake Yeast Saccharomyces cerevisiae Kyokai no. 7 Akao, T.; Yashiro, I.; Hosoyama, A. DNA Research, Vol. 18, Issue 6 https://doi.org/10.1093/dnares/dsr029	journal	September 2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
Draft Genome Sequence of Saccharomyces cerevisiae Strain NCIM3186 Used in the Production of Bioethanol from Sweet Sorghum Sravanthi Goud, Burragoni; Ulaganathan, Kandasamy Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomea.00813-15	journal	July 2015
The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins Borneman, Anthony R.; Desany, Brian A.; Riches, David FEMS Yeast Research, Vol. 12, Issue 1 https://doi.org/10.1111/j.1567-1364.2011.00773.x	journal	December 2011
Structures of Naturally Evolved CUP1 Tandem Arrays in Yeast Indicate That These Arrays Are Generated by Unequal Nonhomologous Recombination Zhao, Ying; Strope, Pooja K.; Kozmin, Stanislav G. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 11 https://doi.org/10.1534/g3.114.012922	journal	September 2014
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology English, Adam C.; Richards, Stephen; Han, Yi PLoS ONE, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pone.0047768	journal	November 2012
The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering Hall, Charles; Dietrich, Fred S. Genetics, Vol. 177, Issue 4 https://doi.org/10.1534/genetics.107.074963	journal	December 2007
Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments Dunn, B.; Richter, C.; Kvitek, D. J. Genome Research, Vol. 22, Issue 5 https://doi.org/10.1101/gr.130310.111	journal	February 2012
Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX™ pretreated corn stover Jin, Mingjie; Sarks, Cory; Gunawan, Christa Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-108	journal	January 2013
Population genomics of domestic and wild yeasts Liti, Gianni; Carter, David M.; Moses, Alan M. Nature, Vol. 458, Issue 7236 https://doi.org/10.1038/nature07743	journal	February 2009
Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast Wei, Na; Quarterman, Josh; Kim, Soo Rin Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3580	journal	October 2013
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads Heo, Yun; Wu, Xiao-Long; Chen, Deming Bioinformatics, Vol. 30, Issue 10 https://doi.org/10.1093/bioinformatics/btu030	journal	January 2014
Combining inhibitor tolerance and D-xylose fermentation in industrial Saccharomyces cerevisiae for efficient lignocellulose-based bioethanol production Demeke, Mekonnen M.; Dumortier, Françoise; Li, Yingying Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-120	journal	January 2013
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome Liti, Gianni; Ba, Alex N. Nguyen; Blythe, Martin BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-69	journal	January 2013
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis Stambuk, B. U.; Dunn, B.; Alves, S. L. Genome Research, Vol. 19, Issue 12 https://doi.org/10.1101/gr.094276.109	journal	November 2009
Organization of the SUC gene family in Saccharomyces. Carlson, M.; Botstein, D. Molecular and Cellular Biology, Vol. 3, Issue 3 https://doi.org/10.1128/MCB.3.3.351	journal	March 1983
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach Proux-Wéra, Estelle; Armisén, David; Byrne, Kevin P. BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-237	journal	January 2012
Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329 Zheng, Dao-Qiong; Wang, Pin-Mei; Chen, Jie BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-479	journal	January 2012
A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes Bergström, Anders; Simpson, Jared T.; Salinas, Francisco Molecular Biology and Evolution, Vol. 31, Issue 4 https://doi.org/10.1093/molbev/msu037	journal	January 2014
The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen Strope, Pooja K.; Skelly, Daniel A.; Kozmin, Stanislav G. Genome Research, Vol. 25, Issue 5 https://doi.org/10.1101/gr.185538.114	journal	April 2015
Yeast Evolution and Comparative Genomics Liti, Gianni; Louis, Edward J. Annual Review of Microbiology, Vol. 59, Issue 1 https://doi.org/10.1146/annurev.micro.59.030804.121400	journal	October 2005
Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover Parreiras, Lucas S.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0107499	journal	September 2014
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus Scannell, Devin R.; Zill, Oliver A.; Rokas, Antonis G3: Genes\|Genomes\|Genetics, Vol. 1, Issue 1 https://doi.org/10.1534/g3.111.000273	journal	June 2011
The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts Baker, EmilyClare; Wang, Bing; Bellora, Nicolas Molecular Biology and Evolution, Vol. 32, Issue 11 https://doi.org/10.1093/molbev/msv168	journal	August 2015
The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now Engel, Stacia R.; Dietrich, Fred S.; Fisk, Dianna G. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 3 https://doi.org/10.1534/g3.113.008995	journal	December 2013
RTM1: a member of a new family of telomeric repeated genes in yeast. Ness, F.; Aigle, M. Genetics, Vol. 140, Issue 3 https://doi.org/10.1093/genetics/140.3.945	journal	July 1995
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, A. Karlsruhe https://doi.org/10.5445/ir/1000045818	text	January 2014
The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions Pool, John E. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msv194	journal	September 2015
Genotype to Phenotype: A Complex Problem Dowell, R. D.; Ryan, O.; Jansen, A. Science, Vol. 328, Issue 5977 https://doi.org/10.1126/science.1189015	journal	April 2010
Genome Sequence of Saccharomyces cerevisiae NCIM3107, Used in Bioethanol Production Ulaganathan, Kandasamy; Sravanthi Goud, Burragoni; Reddy, Mettu Madhavi Genome Announcements, Vol. 3, Issue 1 https://doi.org/10.1128/genomeA.01557-14	journal	February 2015
Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors Piotrowski, Jeff S.; Zhang, Yaoping; Bates, Donna M. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00090	journal	March 2014
Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide-Pretreated Biomass Sato, Trey K.; Liu, Tongjun; Parreiras, Lucas S. Applied and Environmental Microbiology, Vol. 80, Issue 2 https://doi.org/10.1128/AEM.01885-13	journal	November 2013
The yeast IRC7 gene encodes a β-lyase responsible for production of the varietal thiol 4-mercapto-4-methylpentan-2-one in wine Roncoroni, Miguel; Santiago, Margarita; Hooks, David O. Food Microbiology, Vol. 28, Issue 5 https://doi.org/10.1016/j.fm.2011.01.002	journal	August 2011
Multifaceted characterization of cell wall decomposition products formed during ammonia fiber expansion (AFEX) and dilute acid based pretreatments Chundawat, Shishir P. S.; Vismeh, Ramin; Sharma, Lekh N. Bioresource Technology, Vol. 101, Issue 21 https://doi.org/10.1016/j.biortech.2010.06.027	journal	November 2010
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789 Wei, W.; McCusker, J. H.; Hyman, R. W. Proceedings of the National Academy of Sciences, Vol. 104, Issue 31 https://doi.org/10.1073/pnas.0701291104	journal	July 2007
Industrial robust yeast isolates with great potential for fermentation of lignocellulosic biomass Pereira, Francisco B.; Romaní, Aloia; Ruiz, Héctor A. Bioresource Technology, Vol. 161 https://doi.org/10.1016/j.biortech.2014.03.043	journal	June 2014
Organization of the SUC Gene Family in Saccharomyces Carlson, Marian; Botstein, David Molecular and Cellular Biology, Vol. 3, Issue 3 https://doi.org/10.1128/mcb.3.3.351-359.1983	journal	March 1983
SGD: Saccharomyces Genome Database Cherry, J. Nucleic Acids Research, Vol. 26, Issue 1 https://doi.org/10.1093/nar/26.1.73	journal	January 1998
Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short Reads Kamada, Mayumi; Hase, Sumitaka; Sato, Kengo PLoS ONE, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pone.0109999	journal	October 2014
Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 Novo, M.; Bigey, F.; Beyne, E. Proceedings of the National Academy of Sciences, Vol. 106, Issue 38 https://doi.org/10.1073/pnas.0904673106	journal	September 2009
Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass Koppram, Rakesh; Albers, Eva; Olsson, Lisbeth Biotechnology for Biofuels, Vol. 5, Issue 1 https://doi.org/10.1186/1754-6834-5-32	journal	January 2012
Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering Demeke, Mekonnen M.; Dietz, Heiko; Li, Yingying Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-89	journal	January 2013
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 PLoS Genetics, Vol. 7, Issue 2 https://doi.org/10.1371/journal.pgen.1001287	journal	February 2011
Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production Argueso, J. L.; Carazzolle, M. F.; Mieczkowski, P. A. Genome Research, Vol. 19, Issue 12 https://doi.org/10.1101/gr.091777.109	journal	October 2009
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Kearse, M.; Moir, R.; Wilson, A. Bioinformatics, Vol. 28, Issue 12 https://doi.org/10.1093/bioinformatics/bts199	journal	April 2012
Simultaneously improving xylose fermentation and tolerance to lignocellulosic inhibitors through evolutionary engineering of recombinant Saccharomyces cerevisiae harbouring xylose isomerase Smith, Justin; van Rensburg, Eugéne; Görgens, Johann F. BMC Biotechnology, Vol. 14, Issue 1 https://doi.org/10.1186/1472-6750-14-41	journal	January 2014
Cell-wall carbohydrates and their modification as a resource for biofuels Pauly, Markus; Keegstra, Kenneth The Plant Journal, Vol. 54, Issue 4, p. 559-568 https://doi.org/10.1111/j.1365-313X.2008.03463.x	journal	May 2008
Two Duplicated Genes DDI2 and DDI3 in Budding Yeast Encode a Cyanamide Hydratase and Are Induced by Cyanamide Li, Jia; Biss, Michael; Fu, Yu Journal of Biological Chemistry, Vol. 290, Issue 20 https://doi.org/10.1074/jbc.m115.645408	journal	April 2015
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products Nurk, Sergey; Bankevich, Anton; Antipov, Dmitry Journal of Computational Biology, Vol. 20, Issue 10 https://doi.org/10.1089/cmb.2013.0084	journal	October 2013
Reducing assembly complexity of microbial genomes with single-molecule sequencing Koren, Sergey; Harhay, Gregory P.; Smith, Timothy PL Genome Biology, Vol. 14, Issue 9 https://doi.org/10.1186/gb-2013-14-9-r101	journal	January 2013
Genomic Insights into the Saccharomyces sensu stricto Complex Borneman, Anthony R.; Pretorius, Isak S. Genetics, Vol. 199, Issue 2 https://doi.org/10.1534/genetics.114.173633	journal	February 2015
Genealogy of Principal Strains of the Yeast Genetic Stock Center Mortimer, Robert K.; Johnston, John R. Genetics, Vol. 113, Issue 1 https://doi.org/10.1093/genetics/113.1.35	journal	May 1986
Genomics and the making of yeast biodiversity Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan Current Opinion in Genetics & Development, Vol. 35 https://doi.org/10.1016/j.gde.2015.10.008	journal	December 2015
Development of Efficient Xylose Fermentation in Saccharomyces cerevisiae: Xylose Isomerase as a Key Component van Maris, Antonius J. A.; Winkler, Aaron A.; Kuyper, Marko Biofuels, p. 179-204 https://doi.org/10.1007/10_2007_057	book	January 2007
Saccharomyces cerevisiae Σ1278b Has Novel Genes of the N-Acetyltransferase Gene Superfamily Required for l-Proline Analogue Resistance Takagi, Hiroshi; Shichiri, Mika; Takemura, Miho Journal of Bacteriology, Vol. 182, Issue 15 https://doi.org/10.1128/jb.182.15.4249-4256.2000	journal	January 2000
Endogenous Xylose Pathway in Saccharomyces cerevisiae Toivari, M. H.; Salusjarvi, L.; Ruohonen, L. Applied and Environmental Microbiology, Vol. 70, Issue 6 https://doi.org/10.1128/AEM.70.6.3681-3686.2004	journal	June 2004

Cited By (14)

Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts Eldarov, Mikhail A.; Beletsky, Alexey V.; Tanashchuk, Tatiana N. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00965	journal	May 2018
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast Myers, Kevin S.; Riley, Nicholas M.; MacGilvray, Matthew E. PLOS Genetics, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pgen.1008037	journal	March 2019
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations Salazar, Alex N.; Abeel, Thomas Bioinformatics, Vol. 34, Issue 17 https://doi.org/10.1093/bioinformatics/bty614	journal	September 2018
Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts Jacobus, Ana Paula; Stephens, Timothy G.; Youssef, Pierre Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.644089	journal	April 2021
Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae Sato, Trey K.; Tremaine, Mary; Parreiras, Lucas S. PLOS Genetics, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pgen.1006372	journal	October 2016
Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts Gorter de Vries, Arthur R.; Pronk, Jack T.; Daran, Jean-Marc G. Applied and Environmental Microbiology, Vol. 83, Issue 11 https://doi.org/10.1128/aem.03206-16	journal	March 2017
Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network Kuang, Meihua Christina; Hutchins, Paul D.; Russell, Jason D. eLife, Vol. 5 https://doi.org/10.7554/elife.19027	journal	September 2016
Targeting of mitochondrial and cytosolic substrates of tRNA isopentenyltransferases: selection of differential tRNA-i6A37 identity subsets Khalique, Abdul; Mattijssen, Sandy; Haddad, Alexander F. PLOS Genetics https://doi.org/10.1101/714972	journal	July 2019
Long-read sequencing data analysis for yeasts Yue, Jia-Xing; Liti, Gianni Nature Protocols, Vol. 13, Issue 6 https://doi.org/10.1038/nprot.2018.025	journal	May 2018
Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization Salazar, Alex N.; Gorter de Vries, Arthur R.; van den Broek, Marcel BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6263-3	journal	December 2019
Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D Salazar, Alex N.; Gorter de Vries, Arthur R.; van den Broek, Marcel FEMS Yeast Research, Vol. 17, Issue 7 https://doi.org/10.1093/femsyr/fox074	journal	September 2017
Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics Maclean, Calum J.; Metzger, Brian P. H.; Yang, Jian-Rong Molecular Biology and Evolution, Vol. 34, Issue 10 https://doi.org/10.1093/molbev/msx151	journal	May 2017
Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production Peris, David; Moriarty, Ryan V.; Alexander, William G. Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0763-7	journal	March 2017
Recycling RNA-Seq Data to Identify Candidate Orphan Genes for Experimental Analysis Li, Jing; Arendsee, Zebulun; Singh, Urminder Frontiers in Genetics https://doi.org/10.1101/671263	journal	April 2020

Similar Records

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

Journal Article · Tue Nov 21 00:00:00 EST 2017 · The Plant Journal · OSTI ID:1287334

McCormick, Ryan F.; Truong, Sandra K.; Sreedasyam, Avinash; +12 more

Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

Journal Article · Sat Jun 26 00:00:00 EDT 2021 · G3 · OSTI ID:1287334

Skerker, Jeffrey M.; Pianalto, Kaila M.; Mondo, Stephen J.; +6 more

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Journal Article · Thu Mar 12 00:00:00 EDT 2020 · Genome Biology and Evolution · OSTI ID:1287334

Greshake Tzovaras, Bastian; Segers, Francisca H. I. D.; Bicker, Anne; +6 more

Related Subjects

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

Title: Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

Citation Formats

References (78)

Cited By (14)

Similar Records

Related Subjects