A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)
Background: Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover...
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ftunivsantcomp:oai:minerva.usc.es:10347/26042 2023-07-30T04:06:40+02:00 A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) Martínez Portela, Paulino Robledo Sánchez, Diego Taboada Penoucos, Xoana Blanco Hortas, Andrés Moser, Michel Maroso, Francesco Hermida Prieto, Miguel Gómez Tato, Antonio Álvarez Blázquez, Blanca Cabaleiro, Santiago Piferrer, Francesc Bouza Fernández, María Carmen Lien, Sigbjørn Viñas Díaz, Ana María Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física application/pdf http://hdl.handle.net/10347/26042 https://doi.org/10.1016/j.ygeno.2021.04.007 eng eng Elsevier https://doi.org/10.1016/j.ygeno.2021.04.007 info:eu-repo/grantAgreement/EC/H2020/81792 info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2014-57065-R/ES/IDENTIFICACION DEL GEN MAESTRO DETERMINANTE DEL SEXO EN RODABALLO: APLICACIONES INDUSTRIALES PARA LA OBTENCION DE POBLACIONES TODO HEMBRA Genomics 113 (2021) 1705–1718 0888-7543 http://hdl.handle.net/10347/26042 doi:10.1016/j.ygeno.2021.04.007 © 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess Turbot Sex determination GWAS sox2 Interfamily variation Genome assembly Oxford Nanopore info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion ftunivsantcomp https://doi.org/10.1016/j.ygeno.2021.04.007 2023-07-11T23:26:14Z Background: Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. Results: The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. Conclusions: The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families This work was supported by the Spanish Ministry of Economy and Competitiveness, Grant: AGL2014-57065-R, by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 81792 (AQUA-FAANG) and by Consellería de Educación, Universidade e Formación Profesional. Xunta de Galicia, Grant number:ED431C 2018/28 SI Article in Journal/Newspaper Scophthalmus maximus Turbot Minerva - Repositorio institucional da Universidade de Santiago de Compostela (USC) Genomics 113 4 1705 1718 |
institution |
Open Polar |
collection |
Minerva - Repositorio institucional da Universidade de Santiago de Compostela (USC) |
op_collection_id |
ftunivsantcomp |
language |
English |
topic |
Turbot Sex determination GWAS sox2 Interfamily variation Genome assembly Oxford Nanopore |
spellingShingle |
Turbot Sex determination GWAS sox2 Interfamily variation Genome assembly Oxford Nanopore Martínez Portela, Paulino Robledo Sánchez, Diego Taboada Penoucos, Xoana Blanco Hortas, Andrés Moser, Michel Maroso, Francesco Hermida Prieto, Miguel Gómez Tato, Antonio Álvarez Blázquez, Blanca Cabaleiro, Santiago Piferrer, Francesc Bouza Fernández, María Carmen Lien, Sigbjørn Viñas Díaz, Ana María A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
topic_facet |
Turbot Sex determination GWAS sox2 Interfamily variation Genome assembly Oxford Nanopore |
description |
Background: Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. Results: The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. Conclusions: The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families This work was supported by the Spanish Ministry of Economy and Competitiveness, Grant: AGL2014-57065-R, by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 81792 (AQUA-FAANG) and by Consellería de Educación, Universidade e Formación Profesional. Xunta de Galicia, Grant number:ED431C 2018/28 SI |
author2 |
Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física |
format |
Article in Journal/Newspaper |
author |
Martínez Portela, Paulino Robledo Sánchez, Diego Taboada Penoucos, Xoana Blanco Hortas, Andrés Moser, Michel Maroso, Francesco Hermida Prieto, Miguel Gómez Tato, Antonio Álvarez Blázquez, Blanca Cabaleiro, Santiago Piferrer, Francesc Bouza Fernández, María Carmen Lien, Sigbjørn Viñas Díaz, Ana María |
author_facet |
Martínez Portela, Paulino Robledo Sánchez, Diego Taboada Penoucos, Xoana Blanco Hortas, Andrés Moser, Michel Maroso, Francesco Hermida Prieto, Miguel Gómez Tato, Antonio Álvarez Blázquez, Blanca Cabaleiro, Santiago Piferrer, Francesc Bouza Fernández, María Carmen Lien, Sigbjørn Viñas Díaz, Ana María |
author_sort |
Martínez Portela, Paulino |
title |
A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
title_short |
A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
title_full |
A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
title_fullStr |
A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
title_full_unstemmed |
A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) |
title_sort |
genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated zz/zw sex determination of turbot (scophthalmus maximus) |
publisher |
Elsevier |
url |
http://hdl.handle.net/10347/26042 https://doi.org/10.1016/j.ygeno.2021.04.007 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
https://doi.org/10.1016/j.ygeno.2021.04.007 info:eu-repo/grantAgreement/EC/H2020/81792 info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2014-57065-R/ES/IDENTIFICACION DEL GEN MAESTRO DETERMINANTE DEL SEXO EN RODABALLO: APLICACIONES INDUSTRIALES PARA LA OBTENCION DE POBLACIONES TODO HEMBRA Genomics 113 (2021) 1705–1718 0888-7543 http://hdl.handle.net/10347/26042 doi:10.1016/j.ygeno.2021.04.007 |
op_rights |
© 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1016/j.ygeno.2021.04.007 |
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Genomics |
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