A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life Article Swipe
William J. Baker
,
Paul Bailey
,
Vanessa Barber
,
Abigail Barker
,
Sidonie Bellot
,
David Bishop
,
Laura R. Botigué
,
Grace E. 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 Kersey
,
Ilia J. Leitch
,
Félix Forest
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/sysbio/syab035
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/sysbio/syab035
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.]
Related Topics
Concepts
Tree of life (biology)
Phylogenomics
Phylogenetic tree
Biology
Herbarium
Tree (set theory)
Set (abstract data type)
Evolutionary biology
Barcode
Taxon
Phylogenetics
Data set
Ecology
Computer science
Artificial intelligence
Clade
Gene
Programming language
Biochemistry
Mathematics
Operating system
Mathematical analysis
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/sysbio/syab035
- https://academic.oup.com/sysbio/article-pdf/71/2/301/42493380/syab035.pdf
- OA Status
- bronze
- Cited By
- 259
- References
- 83
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3163150242
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3163150242Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/sysbio/syab035Digital Object Identifier
- Title
-
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of LifeWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-05-11Full publication date if available
- Authors
-
William J. Baker, Paul Bailey, Vanessa Barber, Abigail Barker, Sidonie Bellot, David Bishop, Laura R. Botigué, Grace E. 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 Kersey, Ilia J. Leitch, Félix ForestList of authors in order
- Landing page
-
https://doi.org/10.1093/sysbio/syab035Publisher landing page
- PDF URL
-
https://academic.oup.com/sysbio/article-pdf/71/2/301/42493380/syab035.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
bronzeOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/sysbio/article-pdf/71/2/301/42493380/syab035.pdfDirect OA link when available
- Concepts
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Tree of life (biology), Phylogenomics, Phylogenetic tree, Biology, Herbarium, Tree (set theory), Set (abstract data type), Evolutionary biology, Barcode, Taxon, Phylogenetics, Data set, Ecology, Computer science, Artificial intelligence, Clade, Gene, Programming language, Biochemistry, Mathematics, Operating system, Mathematical analysisTop concepts (fields/topics) attached by OpenAlex
- Cited by
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259Total citation count in OpenAlex
- Citations by year (recent)
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2025: 71, 2024: 80, 2023: 69, 2022: 23, 2021: 16Per-year citation counts (last 5 years)
- References (count)
-
83Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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