OREGON STATE UNIVERSITY

“Genome 10K” proposal aims to sequence 10,000 vertebrates

11/04/2009

NEWPORT, Ore. – An international group of scientists is proposing to generate whole genome sequences for 10,000 vertebrate species using technology so new it hasn’t yet been invented. But the scientists say new genome sequencing instruments that will allow them to embark on the project may be available within a year or two.

In preparation, they are identifying collaborators who can help assemble a collection of frozen or otherwise suitably preserved tissues or DNA samples from these species.

Their proposal, called “Genome 10K,” will be published this week in the Journal of Heredity.

“The idea behind the project is to prepare for this third generation of DNA sequencing technology that began with the Humane Genome Project,” said Oregon State University’s Scott Baker, who edits the Journal of Heredity. “Whereas that project took nearly 10 years at a cost of more than $3 billion, the goal now is to sequence an entire genome in less than a week, for a cost of less than $1,000.

“If that happens, the impact would be remarkable,” added Baker. “And it will happen – the only question is, how soon?”

Baker, who is associate director of OSU’s Marine Mammal Institute, is one of more than 50 scientists from around the world who is collaborating on the proposal. He is coordinating the effort to assemble DNA samples for all known species of cetaceans – whales, dolphins and porpoises – a task made more difficult because the exact number of species keeps changing.

As DNA analysis becomes more sophisticated, Baker said, molecular differences are emerging among some animals thought to belong to the same species.

“We are adding a new species every year or two,” Baker said, “and there is some disagreement about what criteria we should use to describe new species. But to date, more than 90 species have been identified and officially recognized that will require tissue or DNA samples.”

Thus far, Baker and his colleagues have viable DNA samples from 87 of those species, stored at OSU’s Hatfield Marine Science Center in Newport, Ore., at the University of Auckland in New Zealand, and at NOAA’s Southwest Fisheries Science Center in La Jolla, Calif., which holds the largest repository of cetacean tissues.

One of the challenges is to obtain samples for rare, endangered and even extinct species, Baker said.

“We have thousands of samples from humpback whales, for example,” he pointed out. “But there are a few cetacean species that are known literally from only a single skull, and it can be tough to extract DNA from that.”

The feasibility of sequencing 10,000 vertebrate genomes “requires only one more order of magnitude reduction in the cost of DNA sequencing, following the four orders of magnitude reduction we have seen in the last 10 years,” the scientists write in their article.

The variety of species identified will present different challenges for genome sequencing, Baker says, and whales, dolphins and porpoises could be among the most difficult.

“With some species of mammals, the computational assembly process is relatively simple – you start with one DNA sequence and stitch it together with an existing sequence that is similar, but not identical,” Baker said. “With whales, though, it is what’s called a ‘de-novo’ assembly. There is no template to follow.

“It’s like a gigantic jigsaw puzzle and you have to figure out where the pieces go,” he added.

 

Baker and his colleagues have been working for nearly 20 years on creating DNA barcodes for different cetacean species. The ability to create entire genome sequences would be of enormous benefits to conservation and basic scientific understanding of cetaceans, he said.

 

“It would give us tremendous new insight into a group of mammals that went through one of the most remarkable adaptations in evolutionary history,” Baker pointed out. “Cetaceans represent an incredible range of ‘extremophiles,’ including the blue whale, which can reach up to 100 feet in length, the bowhead whale, thought to live up to 200 years of age, and the sperm whales, capable of diving to more than a mile in depth.

 

“Yet despite this rapid adaptation in physiology and physical form, the molecular evolution of whales is 10 times slower than in other mammals,” Baked added. “This may help us find out why. The more we learn about how whales and dolphins have evolved – and how they are similar or different in genetic diversity – the better we will be able to protect species driven to the verge of extinction.”

 

The Genome 10K proposal is available free online at the Journal of Heredity, http://jhered.oxfordjournals.org

 Further information is available from the Genome 10K Community of Scientists, http://www.genome10k.org