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dc.contributor.authorBaker, William J.
dc.contributor.authorBailey, Paul
dc.contributor.authorBarber, Vanessa
dc.contributor.authorBarker, Abigail
dc.contributor.authorBellot, Sidonie
dc.contributor.authorBishop, David
dc.contributor.authorBotigué, Laura R.
dc.contributor.authorBrewer, Grace E.
dc.contributor.authorCarruthers, Tom
dc.contributor.authorClarkson, James J.
dc.contributor.authorCook, Jeffrey
dc.contributor.authorCowan, Robyn S.
dc.contributor.authorDodsworth, Steven
dc.contributor.authorEpitawalage, Niroshini
dc.contributor.authorFrançoso, Elaine
dc.contributor.authorGallego, Berta
dc.contributor.authorJohnson, Matthew G.
dc.contributor.authorKim, Jan T.
dc.contributor.authorLeempoel, Kevin
dc.contributor.authorMaurin, Olivier
dc.contributor.authorMcGinnie, Catherine
dc.contributor.authorPokorny, Lisa
dc.contributor.authorRoy, Shyamali
dc.contributor.authorStone, Malcolm
dc.contributor.authorToledo, Eduardo
dc.contributor.authorWickett, Norman J.
dc.contributor.authorZuntini, Alexandre R.
dc.contributor.authorEiserhardt, Wolf L.
dc.contributor.authorKersey, Paul J.
dc.contributor.authorLeitch, Ilia J.
dc.contributor.authorForest, Felix
dc.identifier.citationBaker 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.en_US
dc.description.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 ( ). 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.en_US
dc.publisherOxford University Pressen_US
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International*
dc.subjectSubject Categories::C210 Applied Botanyen_US
dc.titleA comprehensive phylogenomic platform for exploring the angiosperm tree of lifeen_US
dc.contributor.departmentRoyal Botanic Gardens, Kewen_US
dc.contributor.departmentCentre for Research in Agricultural Genomicsen_US
dc.contributor.departmentUniversity of Bedfordshireen_US
dc.contributor.departmentTexas Tech Universityen_US
dc.contributor.departmentUniversity of Hertfordshireen_US
dc.contributor.departmentCentre for Plant Biotechnology and Genomicsen_US
dc.contributor.departmentChicago Botanic Gardenen_US
dc.contributor.departmentAarhus Universityen_US
dc.identifier.journalSystematic Biologyen_US
dc.description.noteGold OA, can add final version when available

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