Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)

Autores
Andersen, Øivind; Rubiolo, Juan Andrés; Pirolli, Davide; Aramburu, Oscar; Pampín, Marina; Righino, Benedetta; Robledo, Diego; Bouza, Carmen; De Rosa, Maria Cristina; Martínez, Paulino
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Non-synonymous variation (NSV) of protein coding genes represents raw material for selection to improve adaptation to the diverse environmental scenarios in wild and livestock populations. Many aquatic species face variations in temperature, salinity and biological factors throughout their distribution range that is reflected by the presence of allelic clines or local adaptation. The turbot (Scophthalmus maximus) is a flatfish of great commercial value with a flourishing aquaculture which has promoted the development of genomic resources. In this study, we developed the first atlas of NSVs in the turbot genome by resequencing 10 individuals from Northeast Atlantic Ocean. More than 50,000 NSVs where detected in the ~ 21,500 coding genes of the turbot genome, and we selected 18 NSVs to be genotyped using a single Mass ARRAY multiplex on 13 wild populations and three turbot farms. We detected signals of divergent selection on several genes related to growth, circadian rhythms, osmoregulation and oxygen binding in the different scenarios evaluated. Furthermore, we explored the impact of NSVs identified on the 3D structure and functional relationship of the correspondent proteins. In summary, our study provides a strategy to identify NSVs in species with consistently annotated and assembled genomes to ascertain their role in adaptation.
Fil: Andersen, Øivind. Norwegian University of Life Sciences; Noruega
Fil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Pirolli, Davide. Norwegian University of Life Sciences; Noruega
Fil: Aramburu, Oscar. Universidad de Santiago de Compostela; España
Fil: Pampín, Marina. Universidad de Santiago de Compostela; España
Fil: Righino, Benedetta. Norwegian University of Life Sciences; Noruega
Fil: Robledo, Diego. Universidad de Santiago de Compostela; España
Fil: Bouza, Carmen. Universidad de Santiago de Compostela; España
Fil: De Rosa, Maria Cristina. Norwegian University of Life Sciences; Noruega
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
Materia
Evolution
Genetic selection
Productive traits
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:11336/240262
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)Andersen, ØivindRubiolo, Juan AndrésPirolli, DavideAramburu, OscarPampín, MarinaRighino, BenedettaRobledo, DiegoBouza, CarmenDe Rosa, Maria CristinaMartínez, PaulinoEvolutionGenetic selectionProductive traitshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Non-synonymous variation (NSV) of protein coding genes represents raw material for selection to improve adaptation to the diverse environmental scenarios in wild and livestock populations. Many aquatic species face variations in temperature, salinity and biological factors throughout their distribution range that is reflected by the presence of allelic clines or local adaptation. The turbot (Scophthalmus maximus) is a flatfish of great commercial value with a flourishing aquaculture which has promoted the development of genomic resources. In this study, we developed the first atlas of NSVs in the turbot genome by resequencing 10 individuals from Northeast Atlantic Ocean. More than 50,000 NSVs where detected in the ~ 21,500 coding genes of the turbot genome, and we selected 18 NSVs to be genotyped using a single Mass ARRAY multiplex on 13 wild populations and three turbot farms. We detected signals of divergent selection on several genes related to growth, circadian rhythms, osmoregulation and oxygen binding in the different scenarios evaluated. Furthermore, we explored the impact of NSVs identified on the 3D structure and functional relationship of the correspondent proteins. In summary, our study provides a strategy to identify NSVs in species with consistently annotated and assembled genomes to ascertain their role in adaptation.Fil: Andersen, Øivind. Norwegian University of Life Sciences; NoruegaFil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Pirolli, Davide. Norwegian University of Life Sciences; NoruegaFil: Aramburu, Oscar. Universidad de Santiago de Compostela; EspañaFil: Pampín, Marina. Universidad de Santiago de Compostela; EspañaFil: Righino, Benedetta. Norwegian University of Life Sciences; NoruegaFil: Robledo, Diego. Universidad de Santiago de Compostela; EspañaFil: Bouza, Carmen. Universidad de Santiago de Compostela; EspañaFil: De Rosa, Maria Cristina. Norwegian University of Life Sciences; NoruegaFil: Martínez, Paulino. Universidad de Santiago de Compostela; EspañaNature2023-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/240262Andersen, Øivind; Rubiolo, Juan Andrés; Pirolli, Davide; Aramburu, Oscar; Pampín, Marina; et al.; Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus); Nature; Scientific Reports; 13; 1; 2-2023; 1-162045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-023-29826-zinfo:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-023-29826-zinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T12:02:39Zoai:ri.conicet.gov.ar:11336/240262instacron: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:34982025-10-22 12:02:39.362CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
title Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
spellingShingle Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
Andersen, Øivind
Evolution
Genetic selection
Productive traits
title_short Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
title_full Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
title_fullStr Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
title_full_unstemmed Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
title_sort Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus)
dc.creator.none.fl_str_mv Andersen, Øivind
Rubiolo, Juan Andrés
Pirolli, Davide
Aramburu, Oscar
Pampín, Marina
Righino, Benedetta
Robledo, Diego
Bouza, Carmen
De Rosa, Maria Cristina
Martínez, Paulino
author Andersen, Øivind
author_facet Andersen, Øivind
Rubiolo, Juan Andrés
Pirolli, Davide
Aramburu, Oscar
Pampín, Marina
Righino, Benedetta
Robledo, Diego
Bouza, Carmen
De Rosa, Maria Cristina
Martínez, Paulino
author_role author
author2 Rubiolo, Juan Andrés
Pirolli, Davide
Aramburu, Oscar
Pampín, Marina
Righino, Benedetta
Robledo, Diego
Bouza, Carmen
De Rosa, Maria Cristina
Martínez, Paulino
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Evolution
Genetic selection
Productive traits
topic Evolution
Genetic selection
Productive traits
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Non-synonymous variation (NSV) of protein coding genes represents raw material for selection to improve adaptation to the diverse environmental scenarios in wild and livestock populations. Many aquatic species face variations in temperature, salinity and biological factors throughout their distribution range that is reflected by the presence of allelic clines or local adaptation. The turbot (Scophthalmus maximus) is a flatfish of great commercial value with a flourishing aquaculture which has promoted the development of genomic resources. In this study, we developed the first atlas of NSVs in the turbot genome by resequencing 10 individuals from Northeast Atlantic Ocean. More than 50,000 NSVs where detected in the ~ 21,500 coding genes of the turbot genome, and we selected 18 NSVs to be genotyped using a single Mass ARRAY multiplex on 13 wild populations and three turbot farms. We detected signals of divergent selection on several genes related to growth, circadian rhythms, osmoregulation and oxygen binding in the different scenarios evaluated. Furthermore, we explored the impact of NSVs identified on the 3D structure and functional relationship of the correspondent proteins. In summary, our study provides a strategy to identify NSVs in species with consistently annotated and assembled genomes to ascertain their role in adaptation.
Fil: Andersen, Øivind. Norwegian University of Life Sciences; Noruega
Fil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Pirolli, Davide. Norwegian University of Life Sciences; Noruega
Fil: Aramburu, Oscar. Universidad de Santiago de Compostela; España
Fil: Pampín, Marina. Universidad de Santiago de Compostela; España
Fil: Righino, Benedetta. Norwegian University of Life Sciences; Noruega
Fil: Robledo, Diego. Universidad de Santiago de Compostela; España
Fil: Bouza, Carmen. Universidad de Santiago de Compostela; España
Fil: De Rosa, Maria Cristina. Norwegian University of Life Sciences; Noruega
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
description Non-synonymous variation (NSV) of protein coding genes represents raw material for selection to improve adaptation to the diverse environmental scenarios in wild and livestock populations. Many aquatic species face variations in temperature, salinity and biological factors throughout their distribution range that is reflected by the presence of allelic clines or local adaptation. The turbot (Scophthalmus maximus) is a flatfish of great commercial value with a flourishing aquaculture which has promoted the development of genomic resources. In this study, we developed the first atlas of NSVs in the turbot genome by resequencing 10 individuals from Northeast Atlantic Ocean. More than 50,000 NSVs where detected in the ~ 21,500 coding genes of the turbot genome, and we selected 18 NSVs to be genotyped using a single Mass ARRAY multiplex on 13 wild populations and three turbot farms. We detected signals of divergent selection on several genes related to growth, circadian rhythms, osmoregulation and oxygen binding in the different scenarios evaluated. Furthermore, we explored the impact of NSVs identified on the 3D structure and functional relationship of the correspondent proteins. In summary, our study provides a strategy to identify NSVs in species with consistently annotated and assembled genomes to ascertain their role in adaptation.
publishDate 2023
dc.date.none.fl_str_mv 2023-02
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/11336/240262
Andersen, Øivind; Rubiolo, Juan Andrés; Pirolli, Davide; Aramburu, Oscar; Pampín, Marina; et al.; Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus); Nature; Scientific Reports; 13; 1; 2-2023; 1-16
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/240262
identifier_str_mv Andersen, Øivind; Rubiolo, Juan Andrés; Pirolli, Davide; Aramburu, Oscar; Pampín, Marina; et al.; Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus); Nature; Scientific Reports; 13; 1; 2-2023; 1-16
2045-2322
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/s41598-023-29826-z
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-023-29826-z
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 Nature
publisher.none.fl_str_mv Nature
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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score 12.982451

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