Researchers launch plan to sequence 66000 species in the United Kingdom. But that's just a start

The red squirrel will be one of the 66,000 species to have its genome sequenced by the Darwin Tree of Life Project.

BarbAnna/Getty Images

By Erik StokstadNov. 1, 2018 , 3:15 PM

LONDON—In the first attempt of its kind, researchers plan to sequence all known species of eukaryotic life—66,000 species of animals, plants, fungi, and protozoa—in a single country, the United Kingdom. The announcement was made here today at the official launch of an even grander $4.7 billion global effort, called the Earth BioGenome Project (EBP), to sequence the genomes of all of Earth’s known 1.5 million species of eukaryotes within a decade.

“We feel it is the next moonshot for biology,” says EBP project chair Harris Lewin, a genomicist at the University of California, Davis. Researchers say the genomes will provide multiple benefits, including new insights into the evolution, assisting in biodiversity conservation, and benefiting agriculture and medicine.

In terms of genomes sequenced, the eukaryotes—the branch of complex life consisting of organisms with cells that have a nucleus inside a membrane—lag far behind the bacteria and archaea. Researchers have sequenced just about 3500 eukaryotic genomes, and only 100 at high quality. In 2015, EBP’s founders hatched the idea to massively expand these numbers. “This was an effort that bubbled up from scientists wanting to know more about how the world works,” says John Kress of the Smithsonian Institution’s National Museum of Natural History in Washington, D.C., a co-chair of the project’s working group.

This group, which includes about 25 scientists, has developed a strategy for coordinating the many efforts around the world that are sequencing the genomes of various taxonomic groups, such as vertebrates or plants, and geographically focused efforts tackling the genomes of key or iconic species found within a single nation’s borders. The project will set standards for genome quality, data curations, and other aspects.

The U.K. sequencing effort—dubbed The Darwin Tree of Life project—will now become part of the EBP mix. The Wellcome Sanger Institute in Hinxton, U.K., says it plans to sequence all known 66,000 species of eukaryotes found within the United Kingdom, except for its overseas territories. Collaborators will include the European Molecular Biology Laboratory in Hinxton, the Royal Botanic Gardens, Kew in the United Kingdom, and the Natural History Museum in London. Sanger will spend up to £50 million over 8 years, about 4% of its annual budget, on the first phase of the project, which will focus on developing the processes for sample collection, R&D on sequencing, and computational methods for assembling the genomes. Sanger director Mike Stratton said he expects another £100 million will be needed over the next 5 to 7 years for the bulk of sample collections and sequencing.

This year, as a proof of principle, and to celebrate its 25th anniversary, the institute sequenced 25 genomes. The list includes a wide range of iconic, cryptic, “flourishing,” and “floundering” species. The starfish proved to be the most difficult, says Sanger’s Daniel Mead, who coordinated the effort. One lesson was that sample preparation—extracting the DNA to sequence—will be one of the more challenging parts of the Darwin project.

Sanger is considering various approaches for how to organize its sequencing work. For example, researchers could select all species within particular taxonomic group, which could inform understanding of their evolution. Another idea is to sequence the genomes of all eukaryotes found within certain places—such as Wytham Woods, a research forest near the University of Oxford in the United Kingdom—where existing ecological knowledge could add value. As with EBP, however, Sanger’s first phase will aim to collect and sequence one representative from each of the 3849 taxonomic families found in the British Isles. “We will be making a major contribution to the Earth BioGenome Project, far greater than the size of the U.K.,” Stratton said.

“I love the ambition” of the Darwin Tree of Life project, says Katherine Belov, a geneticist at The University of Sydney in Australia. “It’s going to be a massive effort.” She hopes it will inspire other countries to do the same. Belov participates in the several projects affiliated with EBP and today announced that Australian institutions will over the next 5 years sequence the genomes of 50 threatened and endangered species.

Also announced today was a memorandum of understanding for participating in EBP. It has been signed by 19 institutions, including BGI Shenzhen, China; the Royal Botanic Gardens, Kew; and Sanger. More than a dozen projects, such as the Global Invertebrate Genomics Alliance, with collaborators at multiple institutions are also affiliated. Coordination is key in achieving such an ambitious goal, Lewin says. “Unless we all take a stake in getting to the end, it will never happen.”

Lewin says the partners now have about a third of the funding on hand to complete the first phase of the EBP project. This phase, which will include sequencing genomes of one species from each of 9000 taxonomic families, should cost about $600 million over 3 years. Lewin expects the rest of the funding for the first phase will be secured within a year. In years 4 to 7, genomes would be sequenced from representatives of each genus, followed by the remainder of the species. “Now, our task is to persuade the National Science Foundation—and a lot of others—that the Earth BioGenome Project will be the next moonshot,” Kress says.

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