Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascert...
| Autores: | , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2016 |
| País: | España |
| Institución: | Universitat Pompeu Fabra |
| Repositorio: | Repositorio Digital de la UPF |
| OAI Identifier: | oai:repositori.upf.edu:10230/27885 |
| Acceso en línea: | http://hdl.handle.net/10230/27885 http://dx.doi.org/10.1093/dnares/dsw007 |
| Access Level: | acceso abierto |
| Palabra clave: | Turbot Genome sequencing Genetic map Genome evolution Productive traits |
| id |
ES_147e8be9f976b3a8a97026a2e03c44df |
|---|---|
| oai_identifier_str |
oai:repositori.upf.edu:10230/27885 |
| network_acronym_str |
ES |
| network_name_str |
España |
| repository_id_str |
|
| spelling |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal lifeFigueras, AntonioCorvelo, AndréGómez Garrido, JèssicaGut, MartaGut, Ivo GlynneMarcet Houben, MarinaVlasova, AnnaHermoso Pulido, AntonioGuigó Serra, RodericGabaldón Estevan, Juan Antonio, 1973-Alioto, TylerMartínez, PaulinoTurbotGenome sequencingGenetic mapGenome evolutionProductive traitsThe turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.This work was funded by the Spanish Government: projects Consolider Ingenio: Aquagenomics (CSD2007-00002) and Metagenoma de la Península Ibérica (CSD2007-00005), Ministerio de Economía y Competitividad and European Regional Development Funds (AGL2012-35904), and Ministerio de Economía y Competitividad (AGL2014-51773 and AGL2014-57065-R); and Local Government Xunta de Galicia (GRC2014/010). P.P. and D.R. gratefully acknowledge the Spanish Ministerio de Educación for their FPU fellowships (AP2010-2408, AP2012-0254). Funding to pay the Open Access publication charges for this article was provided by the Ministerio de Economía y Competitividad (AGL2014-51773) and Xunta de Galicia (GRC2014/010).Oxford University Press201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/27885http://dx.doi.org/10.1093/dnares/dsw007reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésDNA Research. 2016;23(3):181-92info:eu-repo/grantAgreement/ES/1PE/AGL2014-51773info:eu-repo/grantAgreement/ES/1PE/AGL2014-57065-R© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/278852026-06-12T07:21:37Z |
| dc.title.none.fl_str_mv |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| title |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| spellingShingle |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life Figueras, Antonio Turbot Genome sequencing Genetic map Genome evolution Productive traits |
| title_short |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| title_full |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| title_fullStr |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| title_full_unstemmed |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| title_sort |
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life |
| dc.creator.none.fl_str_mv |
Figueras, Antonio Corvelo, André Gómez Garrido, Jèssica Gut, Marta Gut, Ivo Glynne Marcet Houben, Marina Vlasova, Anna Hermoso Pulido, Antonio Guigó Serra, Roderic Gabaldón Estevan, Juan Antonio, 1973- Alioto, Tyler Martínez, Paulino |
| author |
Figueras, Antonio |
| author_facet |
Figueras, Antonio Corvelo, André Gómez Garrido, Jèssica Gut, Marta Gut, Ivo Glynne Marcet Houben, Marina Vlasova, Anna Hermoso Pulido, Antonio Guigó Serra, Roderic Gabaldón Estevan, Juan Antonio, 1973- Alioto, Tyler Martínez, Paulino |
| author_role |
author |
| author2 |
Corvelo, André Gómez Garrido, Jèssica Gut, Marta Gut, Ivo Glynne Marcet Houben, Marina Vlasova, Anna Hermoso Pulido, Antonio Guigó Serra, Roderic Gabaldón Estevan, Juan Antonio, 1973- Alioto, Tyler Martínez, Paulino |
| author2_role |
author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Turbot Genome sequencing Genetic map Genome evolution Productive traits |
| topic |
Turbot Genome sequencing Genetic map Genome evolution Productive traits |
| description |
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2017 2017 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/27885 http://dx.doi.org/10.1093/dnares/dsw007 |
| url |
http://hdl.handle.net/10230/27885 http://dx.doi.org/10.1093/dnares/dsw007 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
DNA Research. 2016;23(3):181-92 info:eu-repo/grantAgreement/ES/1PE/AGL2014-51773 info:eu-repo/grantAgreement/ES/1PE/AGL2014-57065-R |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by-nc/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
http://creativecommons.org/licenses/by-nc/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf application/pdf |
| dc.publisher.none.fl_str_mv |
Oxford University Press |
| publisher.none.fl_str_mv |
Oxford University Press |
| dc.source.none.fl_str_mv |
reponame:Repositorio Digital de la UPF instname:Universitat Pompeu Fabra |
| instname_str |
Universitat Pompeu Fabra |
| reponame_str |
Repositorio Digital de la UPF |
| collection |
Repositorio Digital de la UPF |
| repository.name.fl_str_mv |
|
| repository.mail.fl_str_mv |
|
| _version_ |
1869403739803090944 |
| score |
15,81155 |