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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.
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 po...
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