A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Baker, W. J.; Bailey, P.; Barber, V.; Barker, A.; Bellot, S.; Bishop, D.; Botigue, L. R.; Brewer, G.; Carruthers, T.; Clarkson, J. J.; Cook, J.; Cowan, R. S.; Dodsworth, S.; Epitawalage, N.; Francoso, E.; Gallego, B.; Johnson, M.; Kim, J. T.; Leempoel, K.; Maurin, O.; McGinnie, C.; Pokorny, L.; Roy, S.; Stone, M.; Toledo, E.; Wickett, N. J.; Zuntini, A. R.; Eiserhardt, W. L.; Kersey, P. J.; Leitch, I. J.; Forest, F.

doi:10.1101/2021.02.22.431589

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bioRxiv · 10.1101/2021.02.22.431589

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

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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. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents 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%). Using the multi-species coalescent, we inferred a "first pass" angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with 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. 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 worlds natural history collections.

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Baker, W. J., Bailey, P., Barber, V., Barker, A., Bellot, S., Bishop, D., Botigue, L. R., Brewer, G., Carruthers, T., Clarkson, J. J., Cook, J., Cowan, R. S., Dodsworth, S., Epitawalage, N., Francoso, E., Gallego, B., Johnson, M., Kim, J. T., Leempoel, K., Maurin, O., McGinnie, C., Pokorny, L., Roy, S., Stone, M., Toledo, E., Wickett, N. J., Zuntini, A. R., Eiserhardt, W. L., Kersey, P. J., Leitch, I. J., Forest, F.. 2021-02-22. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. https://doi.org/10.1101/2021.02.22.431589

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