Into the wild: new yeast genomes from natural environments and new tools for their analysis
Abstract
Genomic studies of yeasts from the wild have increased significantly in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. Furthermore, we assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
- Authors:
-
- National Council for Scientific and Technical Research (CONICET)-National Univ. of Comahue, Bariloche (Argentina). Patagonian Andean Inst. of Biological and Geoenvironmental Technologies (IPATEC) and Reference Center for Yeast and Brewing Technology (CRELTEC)
- Spanish National Research Council (CSIC), Valencia (Spain). Inst. of Agrochemistry and Food Technology
- Millennium Inst. for Integrative Biology (iBio), Santiago (Chile); Univ. of Santiago (USACH) (Chile)
- Vanderbilt Univ., Nashville, TN (United States)
- Univ. of Wisconsin, Madison, WI (United States). Center for Genomic Science Innovation, Lab. of Genetics, Wisconsin Energy Inst., J. F. Crow Inst. for the Study of Evolution, and DOE Great Lakes Bioenergy Research Center
- Univ. of Wisconsin, Madison, WI (United States). Center for Genomic Science Innovation, Wisconsin Energy Inst. and J. F. Crow Inst. for the Study of Evolution
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); USDA National Institute of Food and Agriculture; National Scientific and Technical Research Council
- Contributing Org.:
- DOE Great Lakes Bioenergy Research Center
- OSTI Identifier:
- 1600974
- Grant/Contract Number:
- SC0018409; DEB-1442148; PIP11220130100392CO
- Resource Type:
- Accepted Manuscript
- Journal Name:
- FEMS Yeast Research
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 2; Journal ID: ISSN 1567-1356
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Saccharomyces; Hanseniaspora; Phaffia; Biotechnology; Wild yeast
Citation Formats
Libkind, D., Peris, D., Cubillos, F. A., Steenwyk, J. L., Opulente, D. A., Langdon, Q. K., Rokas, A., and Hittinger, C. T. Into the wild: new yeast genomes from natural environments and new tools for their analysis. United States: N. p., 2020.
Web. doi:10.1093/femsyr/foaa008.
Libkind, D., Peris, D., Cubillos, F. A., Steenwyk, J. L., Opulente, D. A., Langdon, Q. K., Rokas, A., & Hittinger, C. T. Into the wild: new yeast genomes from natural environments and new tools for their analysis. United States. https://doi.org/10.1093/femsyr/foaa008
Libkind, D., Peris, D., Cubillos, F. A., Steenwyk, J. L., Opulente, D. A., Langdon, Q. K., Rokas, A., and Hittinger, C. T. Mon .
"Into the wild: new yeast genomes from natural environments and new tools for their analysis". United States. https://doi.org/10.1093/femsyr/foaa008. https://www.osti.gov/servlets/purl/1600974.
@article{osti_1600974,
title = {Into the wild: new yeast genomes from natural environments and new tools for their analysis},
author = {Libkind, D. and Peris, D. and Cubillos, F. A. and Steenwyk, J. L. and Opulente, D. A. and Langdon, Q. K. and Rokas, A. and Hittinger, C. T.},
abstractNote = {Genomic studies of yeasts from the wild have increased significantly in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. Furthermore, we assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.},
doi = {10.1093/femsyr/foaa008},
journal = {FEMS Yeast Research},
number = 2,
volume = 20,
place = {United States},
year = {Mon Feb 03 00:00:00 EST 2020},
month = {Mon Feb 03 00:00:00 EST 2020}
}
Web of Science
Works referenced in this record:
Yeasts from Different Habitats and Their Potential as Biocontrol Agents
journal, April 2018
- Pretscher, Julia; Fischkal, Tilman; Branscheidt, Sina
- Fermentation, Vol. 4, Issue 2
Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes
journal, April 2016
- Wisecaver, Jennifer H.; Alexander, William G.; King, Sean B.
- Molecular Biology and Evolution, Vol. 33, Issue 8
Effect of Temperature on the Prevalence of Saccharomyces Non cerevisiae Species against a S. cerevisiae Wine Strain in Wine Fermentation: Competition, Physiological Fitness, and Influence in Final Wine Composition
journal, February 2017
- Alonso-del-Real, Javier; Lairón-Peris, María; Barrio, Eladio
- Frontiers in Microbiology, Vol. 8
Population structure of mitochondrial genomes in Saccharomyces cerevisiae
journal, June 2015
- Wolters, John F.; Chiu, Kenneth; Fiumera, Heather L.
- BMC Genomics, Vol. 16, Issue 1
Hybridization is a recurrent evolutionary stimulus in wild yeast speciation
journal, February 2019
- Eberlein, Chris; Hénault, Mathieu; Fijarczyk, Anna
- Nature Communications, Vol. 10, Issue 1
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
journal, October 2015
- Goodwin, Sara; Gurtowski, James; Ethe-Sayers, Scott
- Genome Research, Vol. 25, Issue 11
Long-read sequencing data analysis for yeasts
journal, May 2018
- Yue, Jia-Xing; Liti, Gianni
- Nature Protocols, Vol. 13, Issue 6
HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment
journal, July 2016
- Johnson, Matthew G.; Gardner, Elliot M.; Liu, Yang
- Applications in Plant Sciences, Vol. 4, Issue 7
Genome-scale modeling of yeast: chronology, applications and critical perspectives
journal, July 2017
- Lopes, Helder; Rocha, Isabel
- FEMS Yeast Research, Vol. 17, Issue 5
Phylogeography of the wild Lager-brewing ancestor ( Saccharomyces eubayanus ) in Patagonia
journal, October 2018
- Eizaguirre, Juan I.; Peris, David; Rodríguez, María E.
- Environmental Microbiology, Vol. 20, Issue 10
Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair.
journal, March 1994
- Weinert, T. A.; Kiser, G. L.; Hartwell, L. H.
- Genes & Development, Vol. 8, Issue 6
Contrasting evolutionary genome dynamics between domesticated and wild yeasts
journal, April 2017
- Yue, Jia-Xing; Li, Jing; Aigrain, Louise
- Nature Genetics, Vol. 49, Issue 6
Mad1 contribution to spindle assembly checkpoint signalling goes beyond presenting Mad2 at kinetochores
journal, January 2014
- Heinrich, S.; Sewart, K.; Windecker, H.
- EMBO reports, Vol. 15, Issue 3
Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins
journal, July 2018
- Viigand, Katrin; Põšnograjeva, Kristina; Visnapuu, Triinu
- Genes, Vol. 9, Issue 7
Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia
journal, August 2014
- Rodríguez, M. Eugenia; Pérez-Través, Laura; Sangorrín, Marcela P.
- FEMS Yeast Research, Vol. 14, Issue 6
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
journal, May 2019
- Steenwyk, Jacob L.; Opulente, Dana A.; Kominek, Jacek
- PLOS Biology, Vol. 17, Issue 5
Comprehensive Analysis of Hypermutation in Human Cancer
journal, November 2017
- Campbell, Brittany B.; Light, Nicholas; Fabrizio, David
- Cell, Vol. 171, Issue 5
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
journal, May 2013
- Gremme, Gordon; Steinbiss, Sascha; Kurtz, Stefan
- IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 10, Issue 3
Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid
journal, February 2018
- Juergens, Hannes; Varela, Javier A.; Gorter de Vries, Arthur R.
- FEMS Yeast Research, Vol. 18, Issue 3
Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides
journal, March 2016
- Alexander, William G.; Wisecaver, Jennifer H.; Rokas, Antonis
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
Plasmid-Based CRISPR-Cas9 Gene Editing in Multiple Candida Species
journal, March 2019
- Lombardi, Lisa; Oliveira-Pacheco, João; Butler, Geraldine
- mSphere, Vol. 4, Issue 2
Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae
journal, January 2011
- Magwene, Paul M.; Kayıkçı, Ömür; Granek, Joshua A.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 5
Remarkably ancient balanced polymorphisms in a multi-locus gene network
journal, February 2010
- Hittinger, Chris Todd; Gonçalves, Paula; Sampaio, José Paulo
- Nature, Vol. 464, Issue 7285
New yeasts—new brews: modern approaches to brewing yeast design and development
journal, June 2017
- Gibson, B.; Geertman, J. -M. A.; Hittinger, C. T.
- FEMS Yeast Research, Vol. 17, Issue 4
CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications
journal, April 2019
- Cai, Peng; Gao, Jiaoqi; Zhou, Yongjin
- Microbial Cell Factories, Vol. 18, Issue 1
The origin and adaptive evolution of domesticated populations of yeast from Far East Asia
journal, July 2018
- Duan, Shou-Fu; Han, Pei-Jie; Wang, Qi-Ming
- Nature Communications, Vol. 9, Issue 1
The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering
journal, December 2007
- Hall, Charles; Dietrich, Fred S.
- Genetics, Vol. 177, Issue 4
Fermentation innovation through complex hybridization of wild and domesticated yeasts
journal, October 2019
- Langdon, Quinn K.; Peris, David; Baker, EmilyClare P.
- Nature Ecology & Evolution, Vol. 3, Issue 11
Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus
journal, July 2016
- Peris, David; Langdon, Quinn K.; Moriarty, Ryan V.
- PLOS Genetics, Vol. 12, Issue 7
Population genomics of domestic and wild yeasts
journal, February 2009
- Liti, Gianni; Carter, David M.; Moses, Alan M.
- Nature, Vol. 458, Issue 7236
InterProScan 5: genome-scale protein function classification
journal, January 2014
- Jones, P.; Binns, D.; Chang, H. -Y.
- Bioinformatics, Vol. 30, Issue 9
Comparative genomics of biotechnologically important yeasts
journal, August 2016
- Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 35
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae
journal, October 2015
- Strope, Pooja K.; Kozmin, Stanislav G.; Skelly, Daniel A.
- FEMS Yeast Research, Vol. 15, Issue 8
MUMmer4: A fast and versatile genome alignment system
journal, January 2018
- Marçais, Guillaume; Delcher, Arthur L.; Phillippy, Adam M.
- PLOS Computational Biology, Vol. 14, Issue 1
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach
journal, January 2012
- Proux-Wéra, Estelle; Armisén, David; Byrne, Kevin P.
- BMC Bioinformatics, Vol. 13, Issue 1
S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond
journal, March 2015
- Hebly, Marit; Brickwedde, Anja; Bolat, Irina
- FEMS Yeast Research, Vol. 15, Issue 3
Genome Annotation and Curation Using MAKER and MAKER‐P
journal, December 2014
- Campbell, Michael S.; Holt, Carson; Moore, Barry
- Current Protocols in Bioinformatics, Vol. 48, Issue 1
Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast
journal, June 2002
- Jorgensen, P.
- Science, Vol. 297, Issue 5580
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
journal, May 2013
- Hahn, Christoph; Bachmann, Lutz; Chevreux, Bastien
- Nucleic Acids Research, Vol. 41, Issue 13
The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts
journal, August 2015
- Baker, EmilyClare; Wang, Bing; Bellora, Nicolas
- Molecular Biology and Evolution, Vol. 32, Issue 11
Purification and Properties of Yeast Proteases Secreted by Wickerhamomyces anomalus 227 and Metschnikovia pulcherrima 446 during Growth in a White Grape Juice
journal, December 2016
- Schlander, Martina; Distler, Ute; Tenzer, Stefan
- Fermentation, Vol. 3, Issue 1
Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests
journal, December 2015
- Gayevskiy, Velimir; Goddard, Matthew R.
- Environmental Microbiology, Vol. 18, Issue 4
Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers
journal, February 2019
- Cubillos, Francisco A.; Gibson, Brian; Grijalva‐Vallejos, Nubia
- Yeast, Vol. 36, Issue 6
nQuire: a statistical framework for ploidy estimation using next generation sequencing
journal, April 2018
- Weiß, Clemens L.; Pais, Marina; Cano, Liliana M.
- BMC Bioinformatics, Vol. 19, Issue 1
Evidence for a Far East Asian origin of lager beer yeast
journal, May 2014
- Bing, Jian; Han, Pei-Jie; Liu, Wan-Qiu
- Current Biology, Vol. 24, Issue 10
Functional Metabolomics Describes the Yeast Biosynthetic Regulome
journal, October 2016
- Mülleder, Michael; Calvani, Enrica; Alam, Mohammad Tauqeer
- Cell, Vol. 167, Issue 2
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
journal, January 2017
- Istace, Benjamin; Friedrich, Anne; d'Agata, Léo
- GigaScience, Vol. 6, Issue 2
Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae
journal, January 2016
- Barbosa, Raquel; Almeida, Pedro; Safar, Silvana V. B.
- Genome Biology and Evolution, Vol. 8, Issue 2
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
journal, April 2018
- Peter, Jackson; De Chiara, Matteo; Friedrich, Anne
- Nature, Vol. 556, Issue 7701
Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids
journal, April 2014
- Peris, David; Sylvester, Kayla; Libkind, Diego
- Molecular Ecology, Vol. 23, Issue 8
Characterization of Saccharomyces uvarum (Beijerinck, 1898) and related hybrids: assessment of molecular markers that predict the parent and hybrid genomes and a proposal to name yeast hybrids
journal, March 2017
- Nguyen, Huu-Vang; Boekhout, Teun
- FEMS Yeast Research, Vol. 17, Issue 2
Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts
journal, March 2015
- Marsit, Souhir; Mena, Adriana; Bigey, Frédéric
- Molecular Biology and Evolution, Vol. 32, Issue 7
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
journal, June 2017
- Giordano, Francesca; Aigrain, Louise; Quail, Michael A.
- Scientific Reports, Vol. 7, Issue 1
Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118
journal, September 2009
- Novo, M.; Bigey, F.; Beyne, E.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces
journal, July 2012
- League, Garrett P.; Slot, Jason C.; Rokas, Antonis
- FEMS Yeast Research, Vol. 12, Issue 7
Local climatic adaptation in a widespread microorganism
journal, February 2014
- Leducq, Jean-Baptiste; Charron, Guillaume; Samani, Pedram
- Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1777
Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function
journal, April 2019
- Baker, EmilyClare P.; Hittinger, Chris Todd
- PLOS Genetics, Vol. 15, Issue 4
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
journal, May 2017
- Wang, Zhuo; Danziger, Samuel A.; Heavner, Benjamin D.
- PLOS Computational Biology, Vol. 13, Issue 5
Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation
journal, February 2018
- Steenwyk, Jacob L.; Rokas, Antonis
- Frontiers in Microbiology, Vol. 9
Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris
journal, February 2017
- Saitua, Francisco; Torres, Paulina; Pérez-Correa, José Ricardo
- BMC Systems Biology, Vol. 11, Issue 1
Bacterial hypermutation: clinical implications
journal, May 2011
- Jolivet-Gougeon, Anne; Kovacs, Bela; Le Gall-David, Sandrine
- Journal of Medical Microbiology, Vol. 60, Issue 5
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
journal, November 2018
- Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek
- Cell, Vol. 175, Issue 6
Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
journal, February 2014
- Chun, J.; Rainey, F. A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
Recent advances in sequence assembly: principles and applications
journal, April 2017
- Chen, Qingfeng; Lan, Chaowang; Zhao, Liang
- Briefings in Functional Genomics, Vol. 16, Issue 6
Phylogenetic placement of Hanseniaspora-Kloeckera species using multigene sequence analysis with taxonomic implications: descriptions of Hanseniaspora pseudoguilliermondii sp. nov. and Hanseniaspora occidentalis var. citrica var. nov.
journal, May 2006
- Cadez, N.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 5
A new inducible CRISPR‐Cas9 system useful for genome editing and study of double‐strand break repair in Candida glabrata
journal, September 2019
- Maroc, Laetitia; Fairhead, Cécile
- Yeast, Vol. 36, Issue 12
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
journal, April 1999
- Pellegrini, M.; Marcotte, E. M.; Thompson, M. J.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 8
Isolation of thermotolerant yeast Pichia kudriavzevii from nuruk
journal, August 2017
- Choi, Da-Hye; Park, Eun-Hee; Kim, Myoung-Dong
- Food Science and Biotechnology, Vol. 26, Issue 5
Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production
journal, September 2014
- Wohlbach, Dana J.; Rovinskiy, Nikolay; Lewis, Jeffrey A.
- Genome Biology and Evolution, Vol. 6, Issue 9
A Large Set of Newly Created Interspecific Saccharomyces Hybrids Increases Aromatic Diversity in Lager Beers
journal, September 2015
- Mertens, Stijn; Steensels, Jan; Saels, Veerle
- Applied and Environmental Microbiology, Vol. 81, Issue 23
Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts
journal, October 2016
- Gonçalves, Margarida; Pontes, Ana; Almeida, Pedro
- Current Biology, Vol. 26, Issue 20
FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter
journal, August 2010
- Galeote, V.; Novo, M.; Salema-Oom, M.
- Microbiology, Vol. 156, Issue 12
Application of Phylogenetic Networks in Evolutionary Studies
journal, October 2005
- Huson, Daniel H.; Bryant, David
- Molecular Biology and Evolution, Vol. 23, Issue 2
Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution
journal, May 2018
- Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G.
- Molecular Biology and Evolution, Vol. 35, Issue 8
A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum
journal, June 2014
- Almeida, Pedro; Gonçalves, Carla; Teixeira, Sara
- Nature Communications, Vol. 5, Issue 1
Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe
journal, January 2014
- David-Palma, Márcia; Libkind, Diego; Sampaio, José Paulo
- Molecular Ecology, Vol. 23, Issue 4
Novel brewing yeast hybrids: creation and application
journal, November 2016
- Krogerus, Kristoffer; Magalhães, Frederico; Vidgren, Virve
- Applied Microbiology and Biotechnology, Vol. 101, Issue 1
Advances in Industrial Biotechnology Using CRISPR-Cas Systems
journal, February 2018
- Donohoue, Paul D.; Barrangou, Rodolphe; May, Andrew P.
- Trends in Biotechnology, Vol. 36, Issue 2
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
journal, November 2015
- Heavner, Benjamin D.; Price, Nathan D.
- PLOS Computational Biology, Vol. 11, Issue 11
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
journal, March 2019
- Shen, Fangzhou; Sun, Renliang; Yao, Jie
- PLOS Computational Biology, Vol. 15, Issue 3
Deletion of the MAG1 DNA glycosylase gene suppresses alkylation-induced killing and mutagenesis in yeast cells lacking AP endonucleases
journal, December 2001
- Xiao, Wei; Chow, Barbara L.; Hanna, Michelle
- Mutation Research/DNA Repair, Vol. 487, Issue 3-4
Life with 6000 Genes
journal, October 1996
- Goffeau, A.; Barrell, B. G.; Bussey, H.
- Science, Vol. 274, Issue 5287
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9
journal, January 2018
- Akhmetov, Azat; Laurent, Jon; Gollihar, Jimmy
- BIO-PROTOCOL, Vol. 8, Issue 6
Xanthophyllomyces dendrorhous for the industrial production of astaxanthin
journal, August 2010
- Rodríguez-Sáiz, Marta; de la Fuente, Juan Luis; Barredo, José Luis
- Applied Microbiology and Biotechnology, Vol. 88, Issue 3
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma
journal, November 2016
- Bellora, Nicolás; Moliné, Martín; David-Palma, Márcia
- BMC Genomics, Vol. 17, Issue 1
The design of Jemboss: a graphical user interface to EMBOSS
journal, September 2003
- Carver, T.; Bleasby, A.
- Bioinformatics, Vol. 19, Issue 14
Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast
journal, May 2015
- Wu, Baojun; Buljic, Adnan; Hao, Weilong
- Molecular Biology and Evolution, Vol. 32, Issue 10
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast
journal, August 2011
- Libkind, D.; Hittinger, C. T.; Valerio, E.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 35
Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts
journal, January 2019
- Mertens, Stijn; Gallone, Brigida; Steensels, Jan
- PLOS ONE, Vol. 14, Issue 1
A composite genome approach to identify phylogenetically informative data from next-generation sequencing
journal, June 2015
- Schwartz, Rachel S.; Harkins, Kelly M.; Stone, Anne C.
- BMC Bioinformatics, Vol. 16, Issue 1
Expression of the yeast PHR1 gene is induced by DNA-damaging agents.
journal, September 1990
- Sebastian, J.; Kraus, B.; Sancar, G. B.
- Molecular and Cellular Biology, Vol. 10, Issue 9
The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’
journal, June 2017
- Sulo, Pavol; Szabóová, Dana; Bielik, Peter
- DNA Research, Vol. 24, Issue 6
A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes
journal, January 2014
- Bergström, Anders; Simpson, Jared T.; Salinas, Francisco
- Molecular Biology and Evolution, Vol. 31, Issue 4
Factors driving metabolic diversity in the budding yeast subphylum
journal, March 2018
- Opulente, Dana A.; Rollinson, Emily J.; Bernick-Roehr, Cleome
- BMC Biology, Vol. 16, Issue 1
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
journal, January 2018
- Chun, Jongsik; Oren, Aharon; Ventosa, Antonio
- International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 1
Genomics and the making of yeast biodiversity
journal, December 2015
- Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan
- Current Opinion in Genetics & Development, Vol. 35
The fascinating and secret wild life of the budding yeast S. cerevisiae
journal, March 2015
- Liti, Gianni
- eLife, Vol. 4
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica
journal, January 2012
- Loira, Nicolas; Dulermo, Thierry; Nicaud, Jean-Marc
- BMC Systems Biology, Vol. 6, Issue 1
UVB Photoprotective Role of Mycosporines in Yeast: Photostability and Antioxidant Activity of Mycosporine-Glutaminol-Glucoside
journal, January 2011
- Moliné, Martín; Arbeloa, Ernesto M.; Flores, María R.
- Radiation Research, Vol. 175, Issue 1
The yeast 2 μ plasmid: strategies for the survival of a selfish DNA
journal, December 1986
- Mead, David J.; Gardner, David C. J.; Oliver, Stephen G.
- Molecular and General Genetics MGG, Vol. 205, Issue 3
Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
journal, September 2016
- Gallone, Brigida; Steensels, Jan; Prahl, Troels
- Cell, Vol. 166, Issue 6
Speciation driven by hybridization and chromosomal plasticity in a wild yeast
journal, January 2016
- Leducq, Jean-Baptiste; Nielly-Thibault, Lou; Charron, Guillaume
- Nature Microbiology, Vol. 1, Issue 1
Natural mismatch repair mutations mediate phenotypic diversity and drug resistance in Cryptococcus deuterogattii
journal, September 2017
- Billmyre, R. Blake; Clancey, Shelly Applen; Heitman, Joseph
- eLife, Vol. 6
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
journal, December 2017
- Waterhouse, Robert M.; Seppey, Mathieu; Simão, Felipe A.
- Molecular Biology and Evolution, Vol. 35, Issue 3
Biochemical and Thermodynamical Characterization of Glucose Oxidase, Invertase, and Alkaline Phosphatase Secreted by Antarctic Yeasts
journal, December 2017
- Yuivar, Yassef; Barahona, Salvador; Alcaíno, Jennifer
- Frontiers in Molecular Biosciences, Vol. 4
An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data
journal, July 2015
- Fan, Huan; Ives, Anthony R.; Surget-Groba, Yann
- BMC Genomics, Vol. 16, Issue 1
Diverse yeasts for diverse fermented beverages and foods
journal, February 2018
- Hittinger, Chris Todd; Steele, James L.; Ryder, David S.
- Current Opinion in Biotechnology, Vol. 49