5 days ago
Scientists want to sequence all animals, fungi and plants on Earth
The Darwin Tree of Life (DToL) project aims to sequence the genomes of all animals, fungi and plants found in Great Britain and Ireland—some 35,000 in total. That is a colossal undertaking whose first phase is almost complete. Speaking at a meeting of evolutionary biologists held in Beijing on July 23rd, Peter Holland of the University of Oxford told scientists that he and his colleagues had already collected nearly 8,000 species. By December, he added, they hope to have sequenced 3,000 of them (the current count is 2,034).
Collecting high-quality genomes is useful for several purposes. Monitoring conservation, for example. DToL's genome of the pine hoverfly, a critically endangered organism and Britain's rarest native insect, has been used to evaluate the level of inbreeding in populations grown in captivity and reintroduced to the wild. Similar analyses have been performed on the genomes of the Eurasian otter and the chequered skipper butterfly. Such measures allow scientists to assess whether they need to introduce new individuals into a population to widen the gene pool.
There are also medical applications: researchers are now looking for ways to make use of DToL's genome of the scour worm, a livestock parasite, to generate a vaccine. In the future, Dr Holland predicts, researchers will find the instructions for how to build new useful compounds, from antimicrobials to venoms (which are often good starting materials for new drugs), hidden in the genome sequences of other organisms. Such work is already under way at Kew Gardens in London, one of the DToL members, which is looking specifically for new medicinal compounds in newly sequenced fungi.
The project has, in other words, been a momentous success. 'Honestly, we're all jealous of Peter,' says Scott Edwards, a biologist at Harvard University, who studies the evolution of birds. But beyond collecting samples and generating genomes—which are shared freely online—DToL has another function. It is the largest contributor to the Earth Biogenome Project (EBP), a mission to sequence all known eukaryotic life on Earth, meaning all life with complex cells. As a member of this international network, DToL has had a chance not only to build protocols for high-throughput sample collection and genome sequencing, but to share them. Many are now in use around the world.
Of the roughly 1.5m known eukaryotic species that inhabit Earth, DToL's 3,000 genomes are but a fraction. Yet the British project's progress shows that the EBP's grand vision is attainable. Genomic hotspots—in the case of DToL, a woodland in Oxford called Wytham Woods—can provide many of the needed species over a small area. And improvements in sequencing technology mean high-quality genomes can now be generated rapidly and at scale. DToL's next big test will be its second phase, in which the team plans to tackle the remaining species in Great Britain and Ireland.
DToL is one of 61 contributors to the EBP. Other participating projects harvest genomes from everything from iconic African animals to microscopic algae. With so many hands on deck, Harris Lewin from the Arizona State University, who leads the EBP, says he is confident that the grand project will reach the goals of its first phase—10,000 genomes—in 2026 or early 2027. He hopes to see all known eukaryotes sequenced by 2035.
But there are challenges ahead. Funding remains uncertain; DToL, for example, has yet to secure support for its second phase. And sample collection will probably become harder as the lowest-hanging fruit around the world gets picked. Many projects that have so far relied on museum specimens have reached the point where they will now need to go sampling in the wild, says Zhang Guojie from Zhejiang University in China, who helped conceive the EBP and now contributes genomes mainly from birds and primates.
Wild sampling comes not only with the logistical problems of getting to and from remote locations, but also additional layers of bureaucracy. Such samples are subject to the Nagoya protocol, an international treaty that asserts each country's right to negotiate access to the genetic resources of organisms found on their territory. Scientists have to obtain permits and sign benefit-sharing agreements before samples can be collected abroad, hurdles erected as countermeasures to the centuries of rich countries extracting value from the biodiversity of poorer ones.
Though noble in intent, the protocol also creates mountains of confusing bureaucracy for scientists, both in the countries providing samples and those receiving them. 'Researchers around the world end up dealing with heavy burdens they have not been prepared for,' says Aysegul Sirakaya, an independent legal consultant based in Sweden, who specialises in legal questions surrounding the benefit-sharing of biological resources.
Yet Dr Zhang is still optimistic that, once connections are forged, work can progress quickly. 'We have established a group of networks, in Indonesia, in India, in Brazil, lots of those countries where it is very difficult to get access to data or samples,' he says. His team now teaches local scientists, who are exempt from Nagoya restrictions, how to do genomic sequencing and data analysis; other teams have developed mobile gene-sequencers that can be used in places where no such facilities exist. There are plenty of good reasons for optimism. Through a combination of bureaucratic and experimental innovation, the EBP's teams are steadily making progress towards their towering goal.
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