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Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9908912/
https://www.ncbi.nlm.nih.gov/pubmed/36755033
http://dx.doi.org/10.1038/s41467-023-36139-2
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author 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
author_facet 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
author_sort Peris, David
collection PubMed
description 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.
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spelling pubmed-99089122023-02-10 Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces 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 Nat Commun Article 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. Nature Publishing Group UK 2023-02-08 /pmc/articles/PMC9908912/ /pubmed/36755033 http://dx.doi.org/10.1038/s41467-023-36139-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
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
title Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
title_full Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
title_fullStr Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
title_full_unstemmed Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
title_short Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
title_sort macroevolutionary diversity of traits and genomes in the model yeast genus saccharomyces
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9908912/
https://www.ncbi.nlm.nih.gov/pubmed/36755033
http://dx.doi.org/10.1038/s41467-023-36139-2
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