Please use this identifier to cite or link to this item: http://hdl.handle.net/10261/269729
Share/Export:
logo share SHARE BASE
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE
Title

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

AuthorsBaker, William J.; Bailey, Paul; Barber, Vanessa; Barker, Abigail; Bellot, Sidonie; Bishop, David; Botigue, Laura; 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; Forest, Félix
KeywordsBiological sciences
Angiosperms
Angiosperms353
Herbariomics
Museomics
Open access
Target sequence capture
Tree of life
Issue Date18-May-2021
PublisherDryad
CitationBaker, William J.; Bailey, Paul; Barber, Vanessa; Barker, Abigail; Bellot, Sidonie; Bishop, David; Botigue, Laura; 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; Forest, Félix; 2021; A comprehensive phylogenomic platform for exploring the angiosperm tree of life; Dryad; https://doi.org/10.5061/dryad.ns1rn8ps7
AbstractThe 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.
DescriptionSoftware https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife
Publisher version (URL)https://doi.org/10.5061/dryad.ns1rn8ps7
URIhttp://hdl.handle.net/10261/269729
DOI10.5061/dryad.ns1rn8ps7
Appears in Collections:(CRAG) Conjuntos de datos

Files in This Item:
File Description SizeFormat
doi_10.5061_dryad.ns1rn8ps7__v4.zip426,69 MBUnknownView/Open
README.txt3,5 kBTextView/Open
Show full item record
Review this work

Page view(s)

21
checked on Aug 19, 2022

Download(s)

2
checked on Aug 19, 2022

Google ScholarTM

Check

Altmetric

Dimensions


WARNING: Items in Digital.CSIC are protected by copyright, with all rights reserved, unless otherwise indicated.