Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
- Authors:
-
[1];
[2];
[2];
[6];
[7];
[10];
[10];
[11]
more »
- Univ. of Oslo (Norway); Inst. of Agrochemistry and Food Technology (IATA), Valencia (Spain); Univ. of Wisconsin, Madison, WI (United States)
- Univ. of Wisconsin, Madison, WI (United States)
- Univ. of Utrecht (The Netherlands)
- Univ. of Rochester, NY (United States)
- Univ. de Montréal (Canada); Univ. Laval, Quebec City (Canada)
- Canada Natural Resources, Quebec City (Canada)
- Univ. Laval, Quebec City (Canada)
- Científicas y Técnicas (CONICET)-Univ. Nacional del Comahue, Bariloche (Argentina)
- Univ. of Wisconsin, Madison, WI (United States); Univ. NOVA de Lisboa, Caparica (Portugal); Vanderbilt Univ., Nashville, TN (United States)
- Univ. NOVA de Lisboa, Caparica (Portugal)
- Univ. of Wisconsin, Madison, WI (United States); Hebei Univ., Baoding (China)
- Chinese Academy of Sciences (CAS), Beijing (China). Inst. of Chemistry
- Publication Date:
- Research Org.:
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Marie Sklodowska-Curie; Research Council of Norway (RCN); Generalitat Valenciana plan GenT; National Science Foundation (NSF); National Natural Science Foundation of China (NSFC)
- OSTI Identifier:
- 1970475
- Grant/Contract Number:
- SC0018409; FC02-07ER64494; 747775; RCN 324253; 274337; CIDEGENT/2021/039; DGE-1256259; DEB-1253634; DEB−1442148; DEB-2110403; 31770018; 31961133020
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 14; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Evolutionary genetics; Food microbiology; Phylogenetics; Population genetics; Saccharomyces cerevisiae
Citation Formats
Peris, David, Ubbelohde, Emily J., Kuang, Meihua Christina, Kominek, Jacek, Langdon, Quinn K., Adams, Marie, Koshalek, Justin A., Hulfachor, Amanda Beth, Opulente, Dana A., Hall, David J., Hyma, Katie, Fay, Justin C., Leducq, Jean-Baptiste, Charron, Guillaume, Landry, Christian R., Libkind, Diego, Gonçalves, Carla, Gonçalves, Paula, Sampaio, José Paulo, Wang, Qi-Ming, Bai, Feng-Yan, Wrobel, Russel L., and Hittinger, Chris Todd. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. United States: N. p., 2023.
Web. doi:10.1038/s41467-023-36139-2.
Peris, David, Ubbelohde, Emily J., Kuang, Meihua Christina, Kominek, Jacek, Langdon, Quinn K., Adams, Marie, Koshalek, Justin A., Hulfachor, Amanda Beth, Opulente, Dana A., Hall, David J., Hyma, Katie, Fay, Justin C., Leducq, Jean-Baptiste, Charron, Guillaume, Landry, Christian R., Libkind, Diego, Gonçalves, Carla, Gonçalves, Paula, Sampaio, José Paulo, Wang, Qi-Ming, Bai, Feng-Yan, Wrobel, Russel L., & Hittinger, Chris Todd. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. United States. https://doi.org/10.1038/s41467-023-36139-2
Peris, David, Ubbelohde, Emily J., Kuang, Meihua Christina, Kominek, Jacek, Langdon, Quinn K., Adams, Marie, Koshalek, Justin A., Hulfachor, Amanda Beth, Opulente, Dana A., Hall, David J., Hyma, Katie, Fay, Justin C., Leducq, Jean-Baptiste, Charron, Guillaume, Landry, Christian R., Libkind, Diego, Gonçalves, Carla, Gonçalves, Paula, Sampaio, José Paulo, Wang, Qi-Ming, Bai, Feng-Yan, Wrobel, Russel L., and Hittinger, Chris Todd. Wed .
"Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces". United States. https://doi.org/10.1038/s41467-023-36139-2. https://www.osti.gov/servlets/purl/1970475.
@article{osti_1970475,
title = {Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces},
author = {Peris, David and Ubbelohde, Emily J. and Kuang, Meihua Christina and Kominek, Jacek and Langdon, Quinn K. and Adams, Marie and Koshalek, Justin A. and Hulfachor, Amanda Beth and Opulente, Dana A. and Hall, David J. and Hyma, Katie and Fay, Justin C. and Leducq, Jean-Baptiste and Charron, Guillaume and Landry, Christian R. and Libkind, Diego and Gonçalves, Carla and Gonçalves, Paula and Sampaio, José Paulo and Wang, Qi-Ming and Bai, Feng-Yan and Wrobel, Russel L. and Hittinger, Chris Todd},
abstractNote = {Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.},
doi = {10.1038/s41467-023-36139-2},
journal = {Nature Communications},
number = 1,
volume = 14,
place = {United States},
year = {Wed Feb 08 00:00:00 EST 2023},
month = {Wed Feb 08 00:00:00 EST 2023}
}
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