By Allison Proffitt
November 4, 2009 | SINGAPORE—An international team of scientists aims to sequence the genomes of 10,000 vertebrate species, male and female, in a project that could affect every aspect of biology.
Known as the Genome 10K Project, the project was conceived by David Haussler, professor of biomolecular engineering at UC Santa Cruz and a Howard Hughes Medical Institute investigator; Stephen J. O'Brien, chief of the Laboratory of Genomic Diversity at the National Cancer Institute; and Oliver A. Ryder, director of genetics at the San Diego Zoo's Institute for Conservation Research and adjunct professor of biology at UC San Diego.
In April, 55 scientists representing major zoos, museums, research centers and universities around the world hashed out the details. Today almost 70 scientists worldwide are involved and the specifics of the proposal will be published in the Journal of Heredity.
The plan is simple. Gather tissue and DNA specimens from living mammals, birds, reptiles, amphibians, and fishes, and some recently extinct species. When possible, gather data from both males and females, and reflect geographic diversity within a species. Then sequence all of it.
It is a “bold proposal,” says Byrappa Venkatesh, head of the Comparative Genomics Laboratory at Singapore’s Institute of Molecular and Cell Biology and the chairman of the project’s “fish committee.” “The first bottleneck was to identify the species and get hold of tissue samples,” Venkatesh tells Bio-IT World. “We had a meeting in April 2009… and now we’ve cleared that first hurdle. We have more than 10,000 species identified.”
In fact, the group has more than 16,000 proposed species in their database after the April meeting. Venkatesh’s fish committee proposed 4000 species of fish, because fish make up 50% of living vertebrates. The collected samples are housed with more than 50 institutions all over the world.
The results will change the field of biology. The data will lay a foundation for understanding the genetic basis of recent changes within vertebrate species and between closely related species. Results will be analyzed to reveal evolutionary changes and help predict how species will respond to climate change, pollution, emerging diseases, and invasive competitors.
“We are capturing what evolution left us with before the human population started impacting the species—a set of genomes inclusive of the biota that a magnificent evolutionary process has produced,” said lead author Stephen O’Brien.
Now the group, calling themselves the Genome 10K Community of Scientists (G10KCOS), needs to raise money. Funding will hopefully come from the NIH and other agencies, foundations, and conservation groups around the world.
And of course there’s the technology. The Genome 10K committee is counting on the cost of sequencing to fall below $5000. At that price, 10,000 genomes will be possible, but it’s not there yet.
“It was the same when they started the Human Genome Project,” Venkatesh says. “The technology developed in parallel with the project and this will be the same.” Venkatesh says that the group doesn’t have a clear timeline yet, but, “it should take about five years once we have the money and start distributing the samples.”
For Venkatesh, the project has been a long time coming. He has had recent success sequencing the fugu (or pufferfish) and elephant shark genomes, but he’s been hoping for something on a much larger scale. “I’ve been collecting fish samples for the last 16 years,” he says. “I had a list of fishes I wanted to sequence, but we didn’t have the funds. This is what I was hoping for.”