Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora

We present a decade-long research initiative of biodiversity genomics, which aimed at sequencing all vascular plant species occurring in the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region. We detail the sampling and seq...

ver descrição completa

Detalhes bibliográficos
Autores: Lavergne, Sébastien, Pouchon, Charles, Roquet, Cristina, Alberti, Adriana, Boleda, Martí, Perrier, Christophe, Renaud, Julien, Boyer, Frédéric, Bzeznik, Bruno, Rome, Maxime, Douzet, Rollant, Lammers, Youri, Orvain, Céline, Gavory, Frederick, Labadie, Karine, Aubert, Serge, Wincker, Patrick, Valay, Jean-Gabriel, Zimmermann, Niklaus E., Thuiller, Wilfried, Denoeud, France, Alsos, Inger G., Coissac, Eric
Tipo de documento: artigo
Estado:Versión aceptada para publicación
Data de publicação:2025
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/414112
Acesso em linha:http://hdl.handle.net/10261/414112
Access Level:Acesso embargado
Palavra-chave:Biodiversity
Genomics
Arctic–alpine flora
Shotgun sequencing
Barcoding
Phylogenomics
id ES_4350b00e0f8bd9a4b27d4d6f2bfa4f38
oai_identifier_str oai:digital.csic.es:10261/414112
network_acronym_str ES
network_name_str España
repository_id_str
spelling Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine floraLavergne, SébastienPouchon, CharlesRoquet, CristinaAlberti, AdrianaBoleda, MartíPerrier, ChristopheRenaud, JulienBoyer, FrédéricBzeznik, BrunoRome, MaximeDouzet, RollantLammers, YouriOrvain, CélineGavory, FrederickLabadie, KarineAubert, SergeWincker, PatrickValay, Jean-GabrielZimmermann, Niklaus E.Thuiller, WilfriedDenoeud, FranceAlsos, Inger G.Coissac, EricBiodiversityGenomicsArctic–alpine floraShotgun sequencingBarcodingPhylogenomicsWe present a decade-long research initiative of biodiversity genomics, which aimed at sequencing all vascular plant species occurring in the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region. We detail the sampling and sequencing strategies, an online database of genome skimming datasets, and bioinformatic procedures to retrieve sequence data. Based on low coverage shotgun sequencing of 6,105 species, we generated a dataset of 81 orthologous chloroplast loci, including all standard barcodes. Using maximum likelihood, we inferred a species-resolved phylogeny which covers 96% of the flora occurring above treeline in the Alps and 92% of the Arctic Flora, along with many additional non-alpine species to improve species sampling and allow fossil dating. The data released here provide the baseline of a unique, ever-growing genomic resource for various applications such as phylogenomics, systematics, conservation and metabarcoding of the arctic–alpine realm.This work was supported by the French National Research Agency in the framework of the ‘Investissements d’avenir’ program (ANR-15-IDEX-02) by the joint ANR-SNF project Origin-Alps (ANR-16-CE93-0004, SNF-310030L_170059, S.L. and N.E.Z.) and the OSUG@2020 labex (ANR10 LABX56, S.L.). Sampling campaigns were largely funded by the European Research Council under the European Community’s Seventh Framework Programme FP7/2007-2013 grant agreement 281422 (TEEMBIO) and by the SNF grant (31003A_149508). The sequencing was performed within the framework of the PhyloAlps project, funded by France Génomique (ANR-10-INBS-09-08, P.W.), and the PhyloNorway project funded by the Research Council of Norway (226134/F50, I.G.A.) and the Norwegian Biodiversity Information Centre (14-14, 70184209, I.G.A.). The scanning of PhyloAlps herbarium parts was funded by the ANR-GATES (22-EXES-0001). M. Ronikier was supported by the Polish National Science Centre project no. NCN 2020/37/B/NZ8/03307.Peer reviewedTaylor & FrancisAgence Nationale de la Recherche (France)European Research CouncilResearch Council of NorwayNorwegian Biodiversity Information CentreNational Science Centre (Poland)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2026202620252026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/414112reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)http://dx.doi.org/10.1080/23818107.2025.2549565Síinfo:eu-repo/semantics/embargoedAccessoai:digital.csic.es:10261/4141122026-05-22T06:33:51Z
dc.title.none.fl_str_mv Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
title Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
spellingShingle Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
Lavergne, Sébastien
Biodiversity
Genomics
Arctic–alpine flora
Shotgun sequencing
Barcoding
Phylogenomics
title_short Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
title_full Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
title_fullStr Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
title_full_unstemmed Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
title_sort Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
dc.creator.none.fl_str_mv Lavergne, Sébastien
Pouchon, Charles
Roquet, Cristina
Alberti, Adriana
Boleda, Martí
Perrier, Christophe
Renaud, Julien
Boyer, Frédéric
Bzeznik, Bruno
Rome, Maxime
Douzet, Rollant
Lammers, Youri
Orvain, Céline
Gavory, Frederick
Labadie, Karine
Aubert, Serge
Wincker, Patrick
Valay, Jean-Gabriel
Zimmermann, Niklaus E.
Thuiller, Wilfried
Denoeud, France
Alsos, Inger G.
Coissac, Eric
author Lavergne, Sébastien
author_facet Lavergne, Sébastien
Pouchon, Charles
Roquet, Cristina
Alberti, Adriana
Boleda, Martí
Perrier, Christophe
Renaud, Julien
Boyer, Frédéric
Bzeznik, Bruno
Rome, Maxime
Douzet, Rollant
Lammers, Youri
Orvain, Céline
Gavory, Frederick
Labadie, Karine
Aubert, Serge
Wincker, Patrick
Valay, Jean-Gabriel
Zimmermann, Niklaus E.
Thuiller, Wilfried
Denoeud, France
Alsos, Inger G.
Coissac, Eric
author_role author
author2 Pouchon, Charles
Roquet, Cristina
Alberti, Adriana
Boleda, Martí
Perrier, Christophe
Renaud, Julien
Boyer, Frédéric
Bzeznik, Bruno
Rome, Maxime
Douzet, Rollant
Lammers, Youri
Orvain, Céline
Gavory, Frederick
Labadie, Karine
Aubert, Serge
Wincker, Patrick
Valay, Jean-Gabriel
Zimmermann, Niklaus E.
Thuiller, Wilfried
Denoeud, France
Alsos, Inger G.
Coissac, Eric
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.contributor.none.fl_str_mv Agence Nationale de la Recherche (France)
European Research Council
Research Council of Norway
Norwegian Biodiversity Information Centre
National Science Centre (Poland)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Biodiversity
Genomics
Arctic–alpine flora
Shotgun sequencing
Barcoding
Phylogenomics
topic Biodiversity
Genomics
Arctic–alpine flora
Shotgun sequencing
Barcoding
Phylogenomics
description We present a decade-long research initiative of biodiversity genomics, which aimed at sequencing all vascular plant species occurring in the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region. We detail the sampling and sequencing strategies, an online database of genome skimming datasets, and bioinformatic procedures to retrieve sequence data. Based on low coverage shotgun sequencing of 6,105 species, we generated a dataset of 81 orthologous chloroplast loci, including all standard barcodes. Using maximum likelihood, we inferred a species-resolved phylogeny which covers 96% of the flora occurring above treeline in the Alps and 92% of the Arctic Flora, along with many additional non-alpine species to improve species sampling and allow fossil dating. The data released here provide the baseline of a unique, ever-growing genomic resource for various applications such as phylogenomics, systematics, conservation and metabarcoding of the arctic–alpine realm.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/414112
url http://hdl.handle.net/10261/414112
dc.relation.none.fl_str_mv http://dx.doi.org/10.1080/23818107.2025.2549565
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/embargoedAccess
eu_rights_str_mv embargoedAccess
dc.publisher.none.fl_str_mv Taylor & Francis
publisher.none.fl_str_mv Taylor & Francis
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
_version_ 1869407015269302272
score 15,198674

Registros relacionados