A comprehensive phylogenomic platform for exploring the angiosperm tree of life

Baker, W.J. and Bailey, P. and Barber, V. and Barker, A. and Bellot, S. and Bishop, D. and Botigue, L.R. and Brewer, G. and Carruthers, T. and Clarkson, J.J. and Cook, J. and Cowan, R.S. and Dodsworth, Steven and Epitawalage, N. and Françoso, E. and Gallego, B. and Johnson, M.G. and Kim, J.T. and Leempoel, K. and Maurin, O. and Mcginnie, C. and Pokorny, L. and Roy, S. and Stone, M. and Toledo, E. and Wickett, N.J. and Zuntini, A.R. and Eiserhardt, W.L. and Kersey, P.J. and Leitch, I.J. and Forest, F. (2022) A comprehensive phylogenomic platform for exploring the angiosperm tree of life. Systematic Biology 71 (2), pp. 301-319. ISSN 1063-5157.

Abstract

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

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