The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758

The red-legged partridge ( Alectoris rufa) is a socio-economically important game bird in southern Europe. Despite previous efforts, achieving a high-quality, chromosome-level genome assembly has remained challenging. Here, we present a de novo phased, gapless reference genome of A. rufa, combining...

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Autores: Eleiwa, Abderrahmane, Mestre, Pol, Usie, Ana, Vilaprinyo, Ester, Marin-Sanguino, Alberto, Sorribas, Albert, Richart, Cristobal, Salces-Ortiz, Judit, Fernández García, Rosa María, Biarnés, Mar, Antilles, Noélia, Nadal, Jesus, Alves, Rui
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::8ed312b5c0e8fbacd53774de8539aea3
Acceso en línea:http://hdl.handle.net/10261/427342
https://api.elsevier.com/content/abstract/scopus_id/105017415493
Access Level:acceso abierto
Palabra clave:Aves
Birds
Catalan Initiative for the Earth Biogenome Project
Genome assembly
Phasianidae
Reference Genome
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spelling The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758Eleiwa, AbderrahmaneMestre, PolUsie, AnaVilaprinyo, EsterMarin-Sanguino, AlbertoSorribas, AlbertRichart, CristobalSalces-Ortiz, JuditFernández García, Rosa MaríaBiarnés, MarAntilles, NoéliaNadal, JesusAlves, RuiAvesBirdsCatalan Initiative for the Earth Biogenome ProjectGenome assemblyPhasianidaeReference GenomeThe red-legged partridge ( Alectoris rufa) is a socio-economically important game bird in southern Europe. Despite previous efforts, achieving a high-quality, chromosome-level genome assembly has remained challenging. Here, we present a de novo phased, gapless reference genome of A. rufa, combining Nanopore long-read sequencing and Hi-C data from both sexes. The assembly resolves 40 nuclear chromosomes (38 autosomes and the 2 sex chromosomes, Z and W) and the mitochondrial genome, achieving chromosome-scale resolution and 99.1% completeness based on the Aves BUSCO dataset. This high-quality genome provides a critical resource for studying genetic diversity, sex-linked traits, and evolutionary adaptations.AE is the recipients of an industrial Ph. D. fellowship from Generalitat de Catalunya and CESAC. AU acknowledges support by Fundação Nacional para a Ciência e a Tecnologia (FCT), Portugal, through contract grant CEECINST/00100/2021/CP2774/CT0001, and projects UIDB/05183, and LA/P/0121/2020. CR was supported by grant IT20041S from Fundació URV. RF acknowledges support from the following sources of funding: the European Research Council (this project has received funding from the European Research Council (ERC) under the European’s Union’s Horizon 2020 research and innovation programme (grant agreement no. 948281) and the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (AGAUR 2021-SGR00420).Peer reviewedTaylor & FrancisF1000ResearchGeneralitat de CatalunyaFundação para a Ciência e a Tecnologia (Portugal)Fundació URVEuropean Research CouncilEuropean CommissionAgència de Gestió d'Ajuts Universitaris i de RecercaEleiwa, Abderrahmane [0009-0006-0252-9081]Antilles, Noélia [0000-0002-3762-3135]Nadal, Jesus [0000-0002-1875-7242]Alves, Rui [0000-0002-8112-5184]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/427342https://api.elsevier.com/content/abstract/scopus_id/105017415493reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/948281http://dx.doi.org/10.12688/f1000research.162894.1Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::8ed312b5c0e8fbacd53774de8539aea32026-05-22T06:33:51Z
dc.title.none.fl_str_mv The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
title The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
spellingShingle The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
Eleiwa, Abderrahmane
Aves
Birds
Catalan Initiative for the Earth Biogenome Project
Genome assembly
Phasianidae
Reference Genome
title_short The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
title_full The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
title_fullStr The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
title_full_unstemmed The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
title_sort The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
dc.creator.none.fl_str_mv Eleiwa, Abderrahmane
Mestre, Pol
Usie, Ana
Vilaprinyo, Ester
Marin-Sanguino, Alberto
Sorribas, Albert
Richart, Cristobal
Salces-Ortiz, Judit
Fernández García, Rosa María
Biarnés, Mar
Antilles, Noélia
Nadal, Jesus
Alves, Rui
author Eleiwa, Abderrahmane
author_facet Eleiwa, Abderrahmane
Mestre, Pol
Usie, Ana
Vilaprinyo, Ester
Marin-Sanguino, Alberto
Sorribas, Albert
Richart, Cristobal
Salces-Ortiz, Judit
Fernández García, Rosa María
Biarnés, Mar
Antilles, Noélia
Nadal, Jesus
Alves, Rui
author_role author
author2 Mestre, Pol
Usie, Ana
Vilaprinyo, Ester
Marin-Sanguino, Alberto
Sorribas, Albert
Richart, Cristobal
Salces-Ortiz, Judit
Fernández García, Rosa María
Biarnés, Mar
Antilles, Noélia
Nadal, Jesus
Alves, Rui
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Generalitat de Catalunya
Fundação para a Ciência e a Tecnologia (Portugal)
Fundació URV
European Research Council
European Commission
Agència de Gestió d'Ajuts Universitaris i de Recerca
Eleiwa, Abderrahmane [0009-0006-0252-9081]
Antilles, Noélia [0000-0002-3762-3135]
Nadal, Jesus [0000-0002-1875-7242]
Alves, Rui [0000-0002-8112-5184]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Aves
Birds
Catalan Initiative for the Earth Biogenome Project
Genome assembly
Phasianidae
Reference Genome
topic Aves
Birds
Catalan Initiative for the Earth Biogenome Project
Genome assembly
Phasianidae
Reference Genome
description The red-legged partridge ( Alectoris rufa) is a socio-economically important game bird in southern Europe. Despite previous efforts, achieving a high-quality, chromosome-level genome assembly has remained challenging. Here, we present a de novo phased, gapless reference genome of A. rufa, combining Nanopore long-read sequencing and Hi-C data from both sexes. The assembly resolves 40 nuclear chromosomes (38 autosomes and the 2 sex chromosomes, Z and W) and the mitochondrial genome, achieving chromosome-scale resolution and 99.1% completeness based on the Aves BUSCO dataset. This high-quality genome provides a critical resource for studying genetic diversity, sex-linked traits, and evolutionary adaptations.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/427342
https://api.elsevier.com/content/abstract/scopus_id/105017415493
url http://hdl.handle.net/10261/427342
https://api.elsevier.com/content/abstract/scopus_id/105017415493
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/948281
http://dx.doi.org/10.12688/f1000research.162894.1
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Taylor & Francis
F1000Research
publisher.none.fl_str_mv Taylor & Francis
F1000Research
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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