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:
-
[1];
[4];
[4];
[5]
- 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}
}
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- 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
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- 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.
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