A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset]
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 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.
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2022
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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 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. |
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Calleva Foundation 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 |
format |
dataset |
author |
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 |
spellingShingle |
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 A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
author_sort |
Baker, William J. |
title |
A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
title_short |
A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
title_full |
A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
title_fullStr |
A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
title_full_unstemmed |
A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] |
title_sort |
comprehensive phylogenomic platform for exploring the angiosperm tree of life [dataset] |
publisher |
Dryad |
publishDate |
2022 |
url |
http://hdl.handle.net/10261/330558 |
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dig-inia-es-10261-3305582023-07-06T07:20:06Z A comprehensive phylogenomic platform for exploring the angiosperm tree of life [Dataset] 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 Calleva Foundation Dr Mortimer and Theresa Sackler Foundation Garfield Weston Foundation 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 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 Foundation Peer reviewed 2023-07-06T07:16:03Z 2023-07-06T07:16:03Z 2022 dataset Baker, William et al. (2021), A comprehensive phylogenomic platform for exploring the angiosperm tree of life, Dryad, Dataset, https://doi.org/10.5061/dryad.ns1rn8ps7 http://hdl.handle.net/10261/330558 10.5061/dryad.ns1rn8ps7 en http://sftp.kew.org/pub/treeoflife/ https://www.ebi.ac.uk...wser/view/PRJEB35285 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. A comprehensive phylogenomic platform for exploring the angiosperm tree of life. https://doi.org/10.1093/sysbio/syab035. http://hdl.handle.net/10261/279677 Sí open application/zip Dryad |