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Team Publishes Paper on 10K Vertebrate Species Sample Collection Effort

NEW YORK (GenomeWeb News) – In anticipation of whole-genome sequencing and analysis studies to come, an international team is assembling a collection of samples representing more than 10,000 vertebrate species.

The group, which calls itself the "Genome 10K Community of Scientists" or G10KCOS, described the effort in a white paper that's scheduled to appear online tomorrow in the Journal of Heredity.

"[W]e anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future," the team wrote.

The team's "virtual collection" will contain tissue and/or DNA samples that have been collected under Genome 10K guidelines and vouched for through DNA barcoding and other methods. So far the group has set its sights on more than 16,000 vertebrate species.

The effort sprung from the realization that as sequencing costs continue to fall, it will eventually be cheaper to sequence animal genomes than to collect, validate, and store suitable tissue/DNA samples, project co-leader David Haussler, a Howard Hughes Medical Institute investigator and biomolecular engineering researcher at the University of California at Santa Cruz, told GenomeWeb Daily News.

"We decided it would be best to start making this collection now," Haussler said.

The formal G10KCOS consortium sprung from a meeting at the University of California at Santa Cruz this past April. Some 55 individuals from more than 43 research institutions, museums, and zoos attended, Haussler said.

Although the initial goal is to collect enough samples to sequence the whole genomes of 10,000 vertebrate species, the researchers ultimately want to sequence as many vertebrate genomes as they can get their hands on, he added.

"DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry," members of the G10KCOS wrote.

Sample collections and research institutions from around the world have already gotten on board with the project, and the consortium is in the process of putting together a collection of samples from 16,203 vertebrate species. Species selected to date are listed in the group's database.

For his part, project co-leader Oliver Ryder, director of genetics at the San Diego Zoo's Institute for Conservation Research, is helping to ensure that endangered species are adequately represented in the same collection effort.

Sequencing the genomes of endangered species will aid conservation efforts Ryder told GWDN, not only by providing information about disease susceptibility and genetic diversity but also by offering insights into recent evolutionary patterns, demography, and gene flow.

Ryder noted that the San Diego Zoo plans to contribute endangered species samples from its own "frozen zoo", a sample collection built up over about 30 years that contains more than 800 vertebrate taxa.

Haussler said the researchers eventually hope to see all of the vertebrate genomes sequenced to a depth that's on par with the existing dog genome. Even so, the main sequencing effort won't begin until the cost is less than about $3,000 per species, he explained, though the team will likely use existing sequencing technology for a pilot project on a subset of the species.

The G10KCOS members are still working out the details of that pilot, Haussler said, including which species will be sequenced and the technology that will be used for that sequencing.

The researchers are also in the process of securing funding for both the pilot and main arms of the project and are still looking for lead donors for both. Haussler noted that Sydney Brenner has already committed $100,000 in sequencing resources through the Genome Institute of Singapore.

"The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved," Brenner said in a statement. "Genomes contain information from the past — they are molecular fossils — and having sequences from vertebrates will be an essential source of rich information."

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