The newly released high-quality genome of the Canadian lynx should aid in its conservation.
Joel Sartore/Getty Images
In a bid to garner more visibility and support, researchers eager to sequence the genomes of all vertebrates today officially launched the Vertebrate Genomes Project (VGP), releasing 15 very high quality genomes of 14 species. But the group remains far short of raising the funds it will need to document the genomes of the estimated 66,000 vertebrates living on Earth.
The project, which has been underway for 3 years, is a revamp and renaming of an effort begun in 2009 called the Genome 10K Project (G10K), which aimed to decipher the genomes of 10,000 vertebrates. G10K produced about 100 genomes, but they were not very detailed, in part because of the cost of sequencing. Now, however, the cost of high-quality sequencing has dropped to less than $15,000 per billion DNA bases, putting detailed vertebrate genomes within the research community’s reach, says G10K co-founder David Haussler, a computational biologist at the University of California, Santa Cruz. “What we thought was a ‘genome’ back then really wasn’t suitable for in-depth studies,” he explains. “I think we’ve reached a turning point.”
Error-free genomes from a broad sampling of vertebrates will enable researchers “to address questions not possible to [answer] before,” adds neuroscientist Erich Jarvis of The Rockefeller University in New York City, who leads G10K.
Funding remains an obstacle. To date, the VGP has raised $2.5 million of the $6 million needed to sequence a representative species from each of the 260 major branches of the vertebrate family tree. To reach the goal of all 66,000 vertebrates will require about $600 million, Jarvis says.
After Jarvis took charge of G10K in 2017, he set a new course. As he set up a sequencing center at his university, he and colleagues from the Wellcome Sanger Institute in Hinxton, U.K., and the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, sought to bring down sequencing costs by negotiating with sequencing-related companies and developing new protocols and software. The goal was to produce affordable, high-quality genomes that were complete enough to group sequenced DNA bases into individual chromosomes. Eventually, Jarvis says, the VGP aims to produce genomes that exceed the completeness of the human and mouse genomes—which cost billions of dollars to produce.
To illustrate the VGP’s potential, Jarvis and his colleagues today released the 15 high-quality genomes. They include a comprehensive, chromosome-by-chromosome assembly of an endangered New Zealand parrot (a kakapo named “Jane”), a Canadian lynx, a newly discovered turtle species from Mexico, and a legless amphibian called a caecilian. There are two cichlid fish—one is a popular aquarium fish and the other has been the object of extensive evolutionary studies—as well as improved genomes of the zebra finch and platypus.
The VGP has attached some strings to the data. Although researchers who have helped fund or operate the project have unlimited access to the sequences, Jarvis says others will have to agree to limit their studies to one gene across all of the species, or to analyses involving no more than five genes in one species. The restrictions, expected to be in place for at least the next 2 years, are designed to give the VGP consortium time to publish a comprehensive analysis of its sequences.
A similar tiered access policy raised some red flags when it was adapted by researchers documenting the wheat genome. And it prompted some rival groups to scoop the wheat consortium by publishing their own genomes. It’s not clear whether the VGP’s data sharing policies could prompt similar rivalries.
The new genomes are part of a first phase that seeks to sequence 266 species—at least one member of each vertebrate “order,” which the VGP defines as groups that survived or became established after a great extinction event 60 million years ago. The sequencing of 30 species is now underway.
The group developed a priority list of species by asking 20 questions, including questions about the potential contribution that sequencing could make to saving an endangered animal. In some cases, they determined that knowing a vertebrate’s genome could “lower extinction risk,” says Oliver Ryder, a conservation geneticist at the San Diego Zoo in California.
The VGP is seeking government grants and foundation support, but most funding to date has come from individual scientists paying to have their study animal deciphered. And those scientists are flocking to the program, says Jarvis, with the VGP adding about six new species a week to its to-do list. The VGP is now expanding that crowdsourcing model to the general public, with an “Adopt a Species” program and hopes to double the number of species added each week.
Today’s unveiling “is our introduction to the world,” says VGP-G10K Program Director Sadye Paez. “We are hoping that the announcement will generate excitement.”