10.5061/DRYAD.NS1RN8PS7
Baker, William
0000-0001-6727-1831
Royal Botanic Gardens
Bailey, Paul
Royal Botanic Gardens
Barber, Vanessa
Royal Botanic Gardens
Barker, Abigail
Royal Botanic Gardens
Bellot, Sidonie
Royal Botanic Gardens
Bishop, David
Royal Botanic Gardens
Botigue, Laura
Center for Research in Agricultural Genomics
Brewer, Grace
Royal Botanic Gardens
Carruthers, Tom
Royal Botanic Gardens
Clarkson, James
Royal Botanic Gardens
Cook, Jeffrey
Royal Botanic Gardens
Cowan, Robyn
Royal Botanic Gardens
Dodsworth, Steven
University of Bedfordshire
Epitawalage, Niroshini
Royal Botanic Gardens
Françoso, Elaine
Royal Botanic Gardens
Gallego, Berta
Royal Botanic Gardens
Johnson, Matthew
Texas Tech University
Kim, Jan
University of Hertfordshire
Leempoel, Kevin
Royal Botanic Gardens
Maurin, Olivier
Royal Botanic Gardens
Mcginnie, Catherine
Royal Botanic Gardens
Pokorny, Lisa
Centre for Plant Biotechnology and Genomics
Roy, Shyamali
Royal Botanic Gardens
Stone, Malcolm
Royal Botanic Gardens
Toledo, Eduardo
Royal Botanic Gardens
Wickett, Norman
Chicago Botanic Garden
Zuntini, Alexandre
Royal Botanic Gardens
Eiserhardt, Wolf
Aarhus University
Kersey, Paul
Royal Botanic Gardens
Leitch, Ilia
Royal Botanic Gardens
Forest, Félix
Royal Botanic Gardens
Baker, William J
Royal Botanic Gardens
Botigué, Laura R
Royal Botanic Gardens
Clarkson, James J
Royal Botanic Gardens
Cowan, Robyn S
Royal Botanic Gardens
Johnson, Matthew G
Texas Tech University
Kim, Jan T
Royal Botanic Gardens
Wickett, Norman J
Chicago Botanic Garden
Wickett, Norman J
Chicago Botanic Garden
Zuntini, Alexandre R
Royal Botanic Gardens
Zuntini, Alexandre R
Royal Botanic Gardens
Eiserhardt, Wolf L
Royal Botanic Gardens
Eiserhardt, Wolf L
Royal Botanic Gardens
Kersey, Paul J
Royal Botanic Gardens
Kersey, Paul J
Royal Botanic Gardens
Leitch, Ilia J
Royal Botanic Gardens
Leitch, Ilia J
Royal Botanic Gardens
A comprehensive phylogenomic platform for exploring the angiosperm Tree of Life
Dryad
dataset
2021
angiosperms
Angiosperms353
herbariomics
museomics
open access
target sequence capture
tree of life
FOS: Biological sciences
Genetics
Genetics
Ecology, Evolution, Behavior and Systematics
Ecology, Evolution, Behavior and Systematics
Calleva Foundation
https://ror.org/00jwxmn37
The Sackler Trust
https://ror.org/02ehsb520
Garfield Weston Foundation
https://ror.org/00rm5fa18
Royal Botanic Gardens, Kew
Global Tree Seed Bank Programme
2021-05-18T00:00:00Z
2021-05-18T00:00:00Z
en
https://treeoflife.kew.org
http://sftp.kew.org/pub/treeoflife/
https://github.com/RBGKew/KewTreeOfLife
https://www.ebi.ac.uk/ena/browser/view/PRJEB35285
https://doi.org/10.1093/sysbio/syab035
437635522 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.]
See Materials and Methods in corresponding paper.