A comprehensive phylogenomic platform for exploring the angiosperm tree of life

Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife

Detalles Bibliográficos
Autores: Baker, William J., Bailey, Paul, Barber, Vanessa, Barker, Abigail, Bellot, Sidonie, Bishop, David, Botigué, Laura R., Brewer, Grace, Carruthers, Tom, Clarkson, James, Cook, Jeffrey, Cowan, Robyn, Dodsworth, Steven, Epitawalage, Niroshini, Françoso, Elaine, Gallego, Berta, Johnson, Matthew, Kim, Jan, Leempoel, Kevin, Maurin, Olivier, McGinnie, Catherine, Pokorny, Lisa, Roy, Shyamali, Stone, Malcolm, Toledo, Eduardo, Wickett, Norman J., Zuntini, Alexandre, Eiserhardt, Wolf, Kersey, Paul, Leitch, Ilia J., Forest, Félix
Tipo de recurso: conjunto de datos
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/269729
Acceso en línea:http://hdl.handle.net/10261/269729
Access Level:acceso abierto
Palabra clave:Biological sciences
Angiosperms
Angiosperms353
Herbariomics
Museomics
Open access
Target sequence capture
Tree of life
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oai_identifier_str oai:digital.csic.es:10261/269729
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv A comprehensive phylogenomic platform for exploring the angiosperm tree of life
title A comprehensive phylogenomic platform for exploring the angiosperm tree of life
spellingShingle A comprehensive phylogenomic platform for exploring the angiosperm tree of life
Baker, William J.
Biological sciences
Angiosperms
Angiosperms353
Herbariomics
Museomics
Open access
Target sequence capture
Tree of life
title_short A comprehensive phylogenomic platform for exploring the angiosperm tree of life
title_full A comprehensive phylogenomic platform for exploring the angiosperm tree of life
title_fullStr A comprehensive phylogenomic platform for exploring the angiosperm tree of life
title_full_unstemmed A comprehensive phylogenomic platform for exploring the angiosperm tree of life
title_sort A comprehensive phylogenomic platform for exploring the angiosperm tree of life
dc.creator.none.fl_str_mv Baker, William J.
Bailey, Paul
Barber, Vanessa
Barker, Abigail
Bellot, Sidonie
Bishop, David
Botigué, Laura R.
Brewer, Grace
Carruthers, Tom
Clarkson, James
Cook, Jeffrey
Cowan, Robyn
Dodsworth, Steven
Epitawalage, Niroshini
Françoso, Elaine
Gallego, Berta
Johnson, Matthew
Kim, Jan
Leempoel, Kevin
Maurin, Olivier
McGinnie, Catherine
Pokorny, Lisa
Roy, Shyamali
Stone, Malcolm
Toledo, Eduardo
Wickett, Norman J.
Zuntini, Alexandre
Eiserhardt, Wolf
Kersey, Paul
Leitch, Ilia J.
Forest, Félix
author Baker, William J.
author_facet Baker, William J.
Bailey, Paul
Barber, Vanessa
Barker, Abigail
Bellot, Sidonie
Bishop, David
Botigué, Laura R.
Brewer, Grace
Carruthers, Tom
Clarkson, James
Cook, Jeffrey
Cowan, Robyn
Dodsworth, Steven
Epitawalage, Niroshini
Françoso, Elaine
Gallego, Berta
Johnson, Matthew
Kim, Jan
Leempoel, Kevin
Maurin, Olivier
McGinnie, Catherine
Pokorny, Lisa
Roy, Shyamali
Stone, Malcolm
Toledo, Eduardo
Wickett, Norman J.
Zuntini, Alexandre
Eiserhardt, Wolf
Kersey, Paul
Leitch, Ilia J.
Forest, Félix
author_role author
author2 Bailey, Paul
Barber, Vanessa
Barker, Abigail
Bellot, Sidonie
Bishop, David
Botigué, Laura R.
Brewer, Grace
Carruthers, Tom
Clarkson, James
Cook, Jeffrey
Cowan, Robyn
Dodsworth, Steven
Epitawalage, Niroshini
Françoso, Elaine
Gallego, Berta
Johnson, Matthew
Kim, Jan
Leempoel, Kevin
Maurin, Olivier
McGinnie, Catherine
Pokorny, Lisa
Roy, Shyamali
Stone, Malcolm
Toledo, Eduardo
Wickett, Norman J.
Zuntini, Alexandre
Eiserhardt, Wolf
Kersey, Paul
Leitch, Ilia J.
Forest, Félix
author2_role author
author
author
author
author
author
author
author
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 Calleva Foundation
Dr Mortimer and Theresa Sackler Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Biological sciences
Angiosperms
Angiosperms353
Herbariomics
Museomics
Open access
Target sequence capture
Tree of life
topic Biological sciences
Angiosperms
Angiosperms353
Herbariomics
Museomics
Open access
Target sequence capture
Tree of life
description Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife
publishDate 2021
dc.date.none.fl_str_mv 2021
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
Publisher's version
info:eu-repo/semantics/publishedVersion
format dataset
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/269729
url http://hdl.handle.net/10261/269729
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Baker, William J.; Bailey, Paul; Barber, Vanessa; Barker, Abigail; Bellot, Sidonie; Bishop, David; Botigué, Laura R.; Brewer, Grace; Carruthers, Tom; Clarkson, James; Cook, Jeffrey; Cowan, Robyn; Dodsworth, Steven; Epitawalage, Niroshini; Françoso, Elaine; Gallego, Berta; Johnson, Matthew; Kim, Jan; Leempoel, Kevin; Maurin, Olivier; McGinnie, Catherine; Pokorny, Lisa; Roy, Shyamali; Stone, Malcolm; Toledo, Eduardo; Wickett, Norman; Zuntini, Alexandre; Eiserhardt, Wolf; Kersey, Paul; Leitch, Ilia J.; Forest, Félix. Systematic Biology 71(2): 301-319 (2022). https://doi.org/10.1093/sysbio/syab035. http://hdl.handle.net/10261/279677
https://doi.org/10.5061/dryad.ns1rn8ps7
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Dryad
publisher.none.fl_str_mv Dryad
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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spelling A comprehensive phylogenomic platform for exploring the angiosperm tree of lifeBaker, William J.Bailey, PaulBarber, VanessaBarker, AbigailBellot, SidonieBishop, DavidBotigué, Laura R.Brewer, GraceCarruthers, TomClarkson, JamesCook, JeffreyCowan, RobynDodsworth, StevenEpitawalage, NiroshiniFrançoso, ElaineGallego, BertaJohnson, MatthewKim, JanLeempoel, KevinMaurin, OlivierMcGinnie, CatherinePokorny, LisaRoy, ShyamaliStone, MalcolmToledo, EduardoWickett, Norman J.Zuntini, AlexandreEiserhardt, WolfKersey, PaulLeitch, Ilia J.Forest, FélixBiological sciencesAngiospermsAngiosperms353HerbariomicsMuseomicsOpen accessTarget sequence captureTree of lifeSoftware https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLifeThe tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections.Calleva Foundation. Sackler Trust. Garfield Weston FoundationPeer reviewedDryadCalleva FoundationDr Mortimer and Theresa Sackler FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222021info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/269729reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésBaker, William J.; Bailey, Paul; Barber, Vanessa; Barker, Abigail; Bellot, Sidonie; Bishop, David; Botigué, Laura R.; Brewer, Grace; Carruthers, Tom; Clarkson, James; Cook, Jeffrey; Cowan, Robyn; Dodsworth, Steven; Epitawalage, Niroshini; Françoso, Elaine; Gallego, Berta; Johnson, Matthew; Kim, Jan; Leempoel, Kevin; Maurin, Olivier; McGinnie, Catherine; Pokorny, Lisa; Roy, Shyamali; Stone, Malcolm; Toledo, Eduardo; Wickett, Norman; Zuntini, Alexandre; Eiserhardt, Wolf; Kersey, Paul; Leitch, Ilia J.; Forest, Félix. Systematic Biology 71(2): 301-319 (2022). https://doi.org/10.1093/sysbio/syab035. http://hdl.handle.net/10261/279677https://doi.org/10.5061/dryad.ns1rn8ps7Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2697292026-05-22T06:33:51Z
score 15,812429

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