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

Autores
Peris, David; Ubbelohde, Emily J.; Kuang, Meihua Christina; Kominek, Jacek; Langdon, Quinn K.; Adams, María; 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 Frati, Diego; Gonçalves, Carla; Gonçalves, Paula; Sampaio, José Paulo; Wang, Qi-Ming; Bai, Feng-Yan; Wrobel, Russel L.; Hittinger, Chris Todd
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Peris, David. Consejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de Alimentos; España. University of Oslo; Noruega. University of Wisconsin; Estados Unidos
Fil: Ubbelohde, Emily J.. University of Wisconsin; Estados Unidos
Fil: Kuang, Meihua Christina. University of Wisconsin; Estados Unidos
Fil: Kominek, Jacek. University of Wisconsin; Estados Unidos
Fil: Langdon, Quinn K.. University of Wisconsin; Estados Unidos
Fil: Adams, María. University of Wisconsin; Estados Unidos
Fil: Koshalek, Justin A.. University of Wisconsin; Estados Unidos
Fil: Hulfachor, Amanda Beth. University of Wisconsin; Estados Unidos
Fil: Opulente, Dana A.. University of Wisconsin; Estados Unidos
Fil: Hall, David J.. University of Utrecht; Países Bajos
Fil: Hyma, Katie. University of Rochester; Estados Unidos
Fil: Fay, Justin C.. University of Rochester; Estados Unidos
Fil: Leducq, Jean-Baptiste. Laval University; Canadá. University of Montreal; Canadá
Fil: Charron, Guillaume. Laurentian Forestry Centre; Canadá
Fil: Landry, Christian R.. Laval University; Canadá
Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Gonçalves, Carla. Vanderbilt University; Estados Unidos. University of Wisconsin; Estados Unidos. Universidade Nova de Lisboa; Portugal
Fil: Gonçalves, Paula. Universidade Nova de Lisboa; Portugal
Fil: Sampaio, José Paulo. Universidade Nova de Lisboa; Portugal
Fil: Wang, Qi-Ming. University of Wisconsin; Estados Unidos. Hebei University; China
Fil: Bai, Feng-Yan. Chinese Academy of Sciences; República de China
Fil: Wrobel, Russel L.. University of Wisconsin; Estados Unidos
Fil: Hittinger, Chris Todd. University of Wisconsin; Estados Unidos
Materia
YEAST
GENOMIC
SACCHAROMYCES
DIVERSITY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/241016

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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Macroevolutionary diversity of traits and genomes in the model yeast genus SaccharomycesPeris, DavidUbbelohde, Emily J.Kuang, Meihua ChristinaKominek, JacekLangdon, Quinn K.Adams, MaríaKoshalek, Justin A.Hulfachor, Amanda BethOpulente, Dana A.Hall, David J.Hyma, KatieFay, Justin C.Leducq, Jean-BaptisteCharron, GuillaumeLandry, Christian R.Libkind Frati, DiegoGonçalves, CarlaGonçalves, PaulaSampaio, José PauloWang, Qi-MingBai, Feng-YanWrobel, Russel L.Hittinger, Chris ToddYEASTGENOMICSACCHAROMYCESDIVERSITYhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Species 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.Fil: Peris, David. Consejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de Alimentos; España. University of Oslo; Noruega. University of Wisconsin; Estados UnidosFil: Ubbelohde, Emily J.. University of Wisconsin; Estados UnidosFil: Kuang, Meihua Christina. University of Wisconsin; Estados UnidosFil: Kominek, Jacek. University of Wisconsin; Estados UnidosFil: Langdon, Quinn K.. University of Wisconsin; Estados UnidosFil: Adams, María. University of Wisconsin; Estados UnidosFil: Koshalek, Justin A.. University of Wisconsin; Estados UnidosFil: Hulfachor, Amanda Beth. University of Wisconsin; Estados UnidosFil: Opulente, Dana A.. University of Wisconsin; Estados UnidosFil: Hall, David J.. University of Utrecht; Países BajosFil: Hyma, Katie. University of Rochester; Estados UnidosFil: Fay, Justin C.. University of Rochester; Estados UnidosFil: Leducq, Jean-Baptiste. Laval University; Canadá. University of Montreal; CanadáFil: Charron, Guillaume. Laurentian Forestry Centre; CanadáFil: Landry, Christian R.. Laval University; CanadáFil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Gonçalves, Carla. Vanderbilt University; Estados Unidos. University of Wisconsin; Estados Unidos. Universidade Nova de Lisboa; PortugalFil: Gonçalves, Paula. Universidade Nova de Lisboa; PortugalFil: Sampaio, José Paulo. Universidade Nova de Lisboa; PortugalFil: Wang, Qi-Ming. University of Wisconsin; Estados Unidos. Hebei University; ChinaFil: Bai, Feng-Yan. Chinese Academy of Sciences; República de ChinaFil: Wrobel, Russel L.. University of Wisconsin; Estados UnidosFil: Hittinger, Chris Todd. University of Wisconsin; Estados UnidosSpringer2023-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/241016Peris, David; Ubbelohde, Emily J.; Kuang, Meihua Christina; Kominek, Jacek; Langdon, Quinn K.; et al.; Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces; Springer; Nature Communications; 14; 1; 12-2023; 1-192041-1723CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41467-023-36139-2info:eu-repo/semantics/altIdentifier/doi/10.1038/s41467-023-36139-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:56:00Zoai:ri.conicet.gov.ar:11336/241016instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:56:01.082CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv 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
spellingShingle Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
Peris, David
YEAST
GENOMIC
SACCHAROMYCES
DIVERSITY
title_short 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_sort Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
dc.creator.none.fl_str_mv Peris, David
Ubbelohde, Emily J.
Kuang, Meihua Christina
Kominek, Jacek
Langdon, Quinn K.
Adams, María
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 Frati, Diego
Gonçalves, Carla
Gonçalves, Paula
Sampaio, José Paulo
Wang, Qi-Ming
Bai, Feng-Yan
Wrobel, Russel L.
Hittinger, Chris Todd
author Peris, David
author_facet Peris, David
Ubbelohde, Emily J.
Kuang, Meihua Christina
Kominek, Jacek
Langdon, Quinn K.
Adams, María
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 Frati, Diego
Gonçalves, Carla
Gonçalves, Paula
Sampaio, José Paulo
Wang, Qi-Ming
Bai, Feng-Yan
Wrobel, Russel L.
Hittinger, Chris Todd
author_role author
author2 Ubbelohde, Emily J.
Kuang, Meihua Christina
Kominek, Jacek
Langdon, Quinn K.
Adams, María
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 Frati, Diego
Gonçalves, Carla
Gonçalves, Paula
Sampaio, José Paulo
Wang, Qi-Ming
Bai, Feng-Yan
Wrobel, Russel L.
Hittinger, Chris Todd
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv YEAST
GENOMIC
SACCHAROMYCES
DIVERSITY
topic YEAST
GENOMIC
SACCHAROMYCES
DIVERSITY
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Peris, David. Consejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de Alimentos; España. University of Oslo; Noruega. University of Wisconsin; Estados Unidos
Fil: Ubbelohde, Emily J.. University of Wisconsin; Estados Unidos
Fil: Kuang, Meihua Christina. University of Wisconsin; Estados Unidos
Fil: Kominek, Jacek. University of Wisconsin; Estados Unidos
Fil: Langdon, Quinn K.. University of Wisconsin; Estados Unidos
Fil: Adams, María. University of Wisconsin; Estados Unidos
Fil: Koshalek, Justin A.. University of Wisconsin; Estados Unidos
Fil: Hulfachor, Amanda Beth. University of Wisconsin; Estados Unidos
Fil: Opulente, Dana A.. University of Wisconsin; Estados Unidos
Fil: Hall, David J.. University of Utrecht; Países Bajos
Fil: Hyma, Katie. University of Rochester; Estados Unidos
Fil: Fay, Justin C.. University of Rochester; Estados Unidos
Fil: Leducq, Jean-Baptiste. Laval University; Canadá. University of Montreal; Canadá
Fil: Charron, Guillaume. Laurentian Forestry Centre; Canadá
Fil: Landry, Christian R.. Laval University; Canadá
Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Gonçalves, Carla. Vanderbilt University; Estados Unidos. University of Wisconsin; Estados Unidos. Universidade Nova de Lisboa; Portugal
Fil: Gonçalves, Paula. Universidade Nova de Lisboa; Portugal
Fil: Sampaio, José Paulo. Universidade Nova de Lisboa; Portugal
Fil: Wang, Qi-Ming. University of Wisconsin; Estados Unidos. Hebei University; China
Fil: Bai, Feng-Yan. Chinese Academy of Sciences; República de China
Fil: Wrobel, Russel L.. University of Wisconsin; Estados Unidos
Fil: Hittinger, Chris Todd. University of Wisconsin; Estados Unidos
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.
publishDate 2023
dc.date.none.fl_str_mv 2023-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/241016
Peris, David; Ubbelohde, Emily J.; Kuang, Meihua Christina; Kominek, Jacek; Langdon, Quinn K.; et al.; Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces; Springer; Nature Communications; 14; 1; 12-2023; 1-19
2041-1723
CONICET Digital
CONICET
url http://hdl.handle.net/11336/241016
identifier_str_mv Peris, David; Ubbelohde, Emily J.; Kuang, Meihua Christina; Kominek, Jacek; Langdon, Quinn K.; et al.; Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces; Springer; Nature Communications; 14; 1; 12-2023; 1-19
2041-1723
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41467-023-36139-2
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41467-023-36139-2
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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