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A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

View ORCID ProfileWilliam J. Baker, Paul Bailey, Vanessa Barber, Abigail Barker, View ORCID ProfileSidonie Bellot, David Bishop, View ORCID ProfileLaura R. Botigué, Grace Brewer, Tom Carruthers, View ORCID ProfileJames J. Clarkson, Jeffrey Cook, Robyn S. Cowan, View ORCID ProfileSteven Dodsworth, Niroshini Epitawalage, Elaine Françoso, Berta Gallego, View ORCID ProfileMatthew G. Johnson, Jan T. Kim, Kevin Leempoel, Olivier Maurin, Catherine McGinnie, View ORCID ProfileLisa Pokorny, Shyamali Roy, Malcolm Stone, Eduardo Toledo, View ORCID ProfileNorman J. Wickett, View ORCID ProfileAlexandre R. Zuntini, View ORCID ProfileWolf L. Eiserhardt, View ORCID ProfilePaul J. Kersey, View ORCID ProfileIlia J. Leitch, View ORCID ProfileFélix Forest
doi: https://doi.org/10.1101/2021.02.22.431589
William J. Baker
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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  • For correspondence: w.baker@kew.org
Paul Bailey
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Vanessa Barber
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Abigail Barker
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Sidonie Bellot
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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David Bishop
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Laura R. Botigué
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
2Current address: Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
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Grace Brewer
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Tom Carruthers
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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James J. Clarkson
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Jeffrey Cook
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Robyn S. Cowan
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Steven Dodsworth
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
3School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
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Niroshini Epitawalage
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Elaine Françoso
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Berta Gallego
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Matthew G. Johnson
4Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
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Jan T. Kim
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
5Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
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Kevin Leempoel
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Olivier Maurin
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Catherine McGinnie
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Lisa Pokorny
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
6Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
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Shyamali Roy
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Malcolm Stone
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Eduardo Toledo
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Norman J. Wickett
7Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
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Alexandre R. Zuntini
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Wolf L. Eiserhardt
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
8Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
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Paul J. Kersey
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Ilia J. Leitch
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Félix Forest
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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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 world’s natural history collections.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵† Joint senior authors

  • https://treeoflife.kew.org

  • http://sftp.kew.org/pub/treeoflife/

  • https://github.com/RBGKew/KewTreeOfLife

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB35285

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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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 Maurin, Catherine 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
bioRxiv 2021.02.22.431589; doi: https://doi.org/10.1101/2021.02.22.431589
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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 Maurin, Catherine 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
bioRxiv 2021.02.22.431589; doi: https://doi.org/10.1101/2021.02.22.431589

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