A comprehensive phylogenomic platform for exploring the angiosperm tree of life
Authors
Baker, William J.Bailey, Paul
Barber, Vanessa
Barker, Abigail
Bellot, Sidonie
Bishop, David
Botigué, Laura R.
Brewer, Grace E.
Carruthers, Tom
Clarkson, James J.
Cook, Jeffrey
Cowan, Robyn S.
Dodsworth, Steven
Epitawalage, Niroshini
Françoso, Elaine
Gallego, Berta
Johnson, Matthew G.
Kim, Jan T.
Leempoel, Kevin
Maurin, Olivier
McGinnie, Catherine
Pokorny, Lisa
Stone
Roy, Shyamali
Stone, Malcolm
Toledo, Eduardo
Wickett, Norman J.
Zuntini, Alexandre R.
Eiserhardt, Wolf L.
Kersey, Paul J.
Leitch, Ilia J.
Forest, Felix
Affiliation
Royal Botanic Gardens, KewCentre for Research in Agricultural Genomics
University of Bedfordshire
Texas Tech University
University of Hertfordshire
Centre for Plant Biotechnology and Genomics
Chicago Botanic Garden
Aarhus University
Issue Date
2021-05-13
Metadata
Show full item recordAbstract
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.Citation
Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F (2021) 'A comprehensive phylogenomic platform for exploring the angiosperm tree of life', Systematic Biology, 71 (2), pp.301-319.Publisher
Oxford University PressJournal
Systematic BiologyPubMed ID
33983440PubMed Central ID
PMC8830076Additional Links
https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syab035/6275244https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830076/
Type
ArticleLanguage
enISSN
1063-5157EISSN
1076-836Xae974a485f413a2113503eed53cd6c53
10.1093/sysbio/syab035
Scopus Count
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- Creative Commons
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