A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

William J. Baker, Paul Bailey, Vanessa Barber, Abigail Barker, Sidonie Bellot, David Bishop, Laura R. Botigué, Grace Brewer, Tom Carruthers, James J. Clarkson, Jeffrey Cook, Robyn S. Cowan, Steven Dodsworth, Niroshini Epitawalage, Elaine Françoso, Berta Gallego, Matthew G. Johnson, Jan T. Kim, Kevin Leempoel, Olivier MaurinCatherine McGinnie, Lisa Pokorny, Shyamali Roy, Malcolm Stone, Eduardo Toledo, Norman J. Wickett, Alexandre R. Zuntini, Wolf L. Eiserhardt, Paul J. Kersey, Ilia J. Leitch, Félix Forest

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

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 article 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 data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A "first pass"angiosperm tree of life was inferred from the data, which totaled 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 data set, 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 toward 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 standardized 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. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]

Original languageEnglish
Pages (from-to)301-319
Number of pages19
JournalSystematic biology
Volume71
Issue number2
DOIs
StatePublished - Mar 1 2022

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