A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life
The 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 seq...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Universitat Autònoma de Barcelona |
| Repositorio: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglés |
| OAI Identifier: | oai:ddd.uab.cat:256111 |
| Acceso en línea: | https://ddd.uab.cat/record/256111 https://dx.doi.org/urn:doi:10.1093/sysbio/syab035 |
| Access Level: | acceso abierto |
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| 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..|||0000-0001-6727-1831 |
| 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..|||0000-0001-6727-1831 Bailey, Paul C|||0000-0002-4650-9668 Barber, Vanessa Barker, Abigail Bellot, Sidonie|||0000-0001-6355-237X Bishop, David Botigué, Laura|||0000-0001-7114-5168 Brewer, Grace Carruthers, Tom Clarkson, James J. Cook, Jeffrey Cowan, Robyn S. Dodsworth, Steven|||0000-0001-6531-3540 Epitawalage, Niroshini Françoso, Elaine|||0000-0002-6464-1240 Gallego Páramo, Berta|||0000-0002-2016-7161 Johnson, Matthew G.|||0000-0002-1958-6334 Kim, Jan T. Leempoel, Kevin|||0000-0001-7335-7930 Maurin, Olivier|||0000-0002-4151-6164 Mcginnie, Catherine Pokorny, Lisa|||0000-0002-2478-8555 Roy, Shyamali Stone, Malcolm Toledo, Eduardo Wickett, Norman J.|||0000-0003-0944-1956 Zuntini, Alexandre R.|||0000-0003-0705-8902 Eiserhardt, Wolf L.|||0000-0002-8136-5233 Kersey, Paul J.|||0000-0002-7054-800X Leitch, Ilia J.|||0000-0002-3837-8186 Forest, Félix|||0000-0002-2004-433X |
| author |
Baker, William J..|||0000-0001-6727-1831 |
| author_facet |
Baker, William J..|||0000-0001-6727-1831 Bailey, Paul C|||0000-0002-4650-9668 Barber, Vanessa Barker, Abigail Bellot, Sidonie|||0000-0001-6355-237X Bishop, David Botigué, Laura|||0000-0001-7114-5168 Brewer, Grace Carruthers, Tom Clarkson, James J. Cook, Jeffrey Cowan, Robyn S. Dodsworth, Steven|||0000-0001-6531-3540 Epitawalage, Niroshini Françoso, Elaine|||0000-0002-6464-1240 Gallego Páramo, Berta|||0000-0002-2016-7161 Johnson, Matthew G.|||0000-0002-1958-6334 Kim, Jan T. Leempoel, Kevin|||0000-0001-7335-7930 Maurin, Olivier|||0000-0002-4151-6164 Mcginnie, Catherine Pokorny, Lisa|||0000-0002-2478-8555 Roy, Shyamali Stone, Malcolm Toledo, Eduardo Wickett, Norman J.|||0000-0003-0944-1956 Zuntini, Alexandre R.|||0000-0003-0705-8902 Eiserhardt, Wolf L.|||0000-0002-8136-5233 Kersey, Paul J.|||0000-0002-7054-800X Leitch, Ilia J.|||0000-0002-3837-8186 Forest, Félix|||0000-0002-2004-433X |
| author_role |
author |
| author2 |
Bailey, Paul C|||0000-0002-4650-9668 Barber, Vanessa Barker, Abigail Bellot, Sidonie|||0000-0001-6355-237X Bishop, David Botigué, Laura|||0000-0001-7114-5168 Brewer, Grace Carruthers, Tom Clarkson, James J. Cook, Jeffrey Cowan, Robyn S. Dodsworth, Steven|||0000-0001-6531-3540 Epitawalage, Niroshini Françoso, Elaine|||0000-0002-6464-1240 Gallego Páramo, Berta|||0000-0002-2016-7161 Johnson, Matthew G.|||0000-0002-1958-6334 Kim, Jan T. Leempoel, Kevin|||0000-0001-7335-7930 Maurin, Olivier|||0000-0002-4151-6164 Mcginnie, Catherine Pokorny, Lisa|||0000-0002-2478-8555 Roy, Shyamali Stone, Malcolm Toledo, Eduardo Wickett, Norman J.|||0000-0003-0944-1956 Zuntini, Alexandre R.|||0000-0003-0705-8902 Eiserhardt, Wolf L.|||0000-0002-8136-5233 Kersey, Paul J.|||0000-0002-7054-800X Leitch, Ilia J.|||0000-0002-3837-8186 Forest, Félix|||0000-0002-2004-433X |
| 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 |
| description |
The 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 article 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 (). 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 data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96) and 2333 genera (17). A "first pass" angiosperm tree of life was inferred from the data, which totaled 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 data set, 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 toward 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 standardized 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. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.] |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2 2021-01-01 2021 2021-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
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article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/256111 https://dx.doi.org/urn:doi:10.1093/sysbio/syab035 |
| url |
https://ddd.uab.cat/record/256111 https://dx.doi.org/urn:doi:10.1093/sysbio/syab035 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona |
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Universitat Autònoma de Barcelona |
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Dipòsit Digital de Documents de la UAB |
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Dipòsit Digital de Documents de la UAB |
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A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of LifeBaker, William J..|||0000-0001-6727-1831Bailey, Paul C|||0000-0002-4650-9668Barber, VanessaBarker, AbigailBellot, Sidonie|||0000-0001-6355-237XBishop, DavidBotigué, Laura|||0000-0001-7114-5168Brewer, GraceCarruthers, TomClarkson, James J.Cook, JeffreyCowan, Robyn S.Dodsworth, Steven|||0000-0001-6531-3540Epitawalage, NiroshiniFrançoso, Elaine|||0000-0002-6464-1240Gallego Páramo, Berta|||0000-0002-2016-7161Johnson, Matthew G.|||0000-0002-1958-6334Kim, Jan T.Leempoel, Kevin|||0000-0001-7335-7930Maurin, Olivier|||0000-0002-4151-6164Mcginnie, CatherinePokorny, Lisa|||0000-0002-2478-8555Roy, ShyamaliStone, MalcolmToledo, EduardoWickett, Norman J.|||0000-0003-0944-1956Zuntini, Alexandre R.|||0000-0003-0705-8902Eiserhardt, Wolf L.|||0000-0002-8136-5233Kersey, Paul J.|||0000-0002-7054-800XLeitch, Ilia J.|||0000-0002-3837-8186Forest, Félix|||0000-0002-2004-433XThe 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 article 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 (). 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 data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96) and 2333 genera (17). A "first pass" angiosperm tree of life was inferred from the data, which totaled 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 data set, 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 toward 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 standardized 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. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.] 22021-01-0120212021-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/256111https://dx.doi.org/urn:doi:10.1093/sysbio/syab035reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2561112026-06-06T12:50:31Z |
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15.301629 |