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Plant genomics: Huge database includes over 9000 species of flowering plants

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Public library of DNA sequences will allow botanists to track the complex evolutionary history of flowering plants in unprecedented detail



Life



1 February 2022

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Zinnia flowers in a meadow

Shutterstock / Pheobus

More than 9000 species of plants have had sections of their genomes sequenced as part of the Plant and Fungal Trees of Life (PAFTOL) project led by the Royal Botanic Gardens, Kew in the UK. This is the largest genetic database of flowering plants ever built, and it could help botanists to identify and conserve species under threat.

Plants that fruit or flower are called angiosperms and make up the vast majority of plant life on Earth, except for the groups that contain conifers, ferns and mosses. They play a vital role across terrestrial ecosystems, storing substantial amounts of carbon and producing vast amounts of oxygen. They also make up most of the calories we ingest.

In 2016, researchers at Kew began an effort to complete the trees of life – descriptions of the evolutionary relationships between organisms – for all genera of plants and fungi. The first phase of this has focused on flowering plants, which comprise around 13,600 genera.

Rather than sequencing whole genomes, William Baker at Kew and his colleagues targeted 353 specific genes that can be found in all green plants.

“Having a whole genome doesn’t always do you many favours. You end up with a vast computational challenge,” says Baker. The team designed a set of probes – short strands of DNA that search for complementary sequences in genes they wanted to target, which give them enough information to establish the relationships between the species.

The project has now compiled genetic codes from 9823 flowering plant specimens. These specimens represent 99 per cent of all flowering plant families, as well as 55 per cent of all flowering plant genera – many of which had never been sequenced before. This accounts for 9404 unique species out of the roughly 340,000 angiosperm species that are thought to exist.

Next, the team mapped out where each genus – and where possible, each species – of flowering plant sits on the tree of life by comparing similarities in their gene sequences.

The project marks a major milestone in plant science, says Baker. With unparalleled coverage of known plant biodiversity, we can now track the complex evolutionary history of flowering plants in unprecedented detail, he says.

“I regard the tree of life as akin to the periodic table,” he says. “It’s the basic road map, the rule book for life on Earth.”

All the data is publicly accessible from the Kew Tree of Life Explorer. As to its applications, the sky is the limit, says Baker.

Scientists at Kew are already beginning to use the data to explore plant genomes for potential medicinal molecules, and predict the susceptibility of trees to novel pests that are expected to arrive in the UK soon.

Knowing the evolutionary relationships between plants could help scientists predict which ones may be most vulnerable, he says, and develop conservation strategies.

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