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Researchers Sequencing Tasmanian Devil Genomes with an Eye Toward Conservation

By Andrea Anderson

SAN DIEGO (GenomeWeb News) – Using genome sequencing and other strategies, researchers from Pennsylvania State University and elsewhere are finding genetic clues that they say may be useful for selecting Tasmanian devils for breeding programs aimed at saving the animals from extinction.

The team used Roche 454 technology to do de novo sequencing of two Tasmanian devil genomes, Penn State biochemistry and molecular biology researcher Stephan Schuster said during Roche Applied Science workshop at the Plant and Animal Genomes conference here this week.

By looking at SNP data in the nuclear and mitochondrial genomes of Tasmanian devils, he explained, the team is tracking down informative markers that they believe may be useful for gauging genetic diversity and managing Tasmanian devil populations through more tailored breeding programs.

For instance, Schuster said, he and his team estimate that far fewer animals would be needed for breeding programs if devils were selected based on genetic information. The need for successful breeding programs has become more pressing in recent years, he explained, as researchers and conservationists work to protect the Tasmanian devil from a deadly infectious cancer that has decimated wild populations.

The Tasmanian devil facial tumor disease is passed from one devil to another when the animals bite each other during feeding and mating. It was first detected in the mid-1990s, Schuster noted, and by 2006 it had reduced wild devil populations by 60 percent or more. Consequently, the animals are currently classified as endangered and may disappear if significant steps are not taken.

"We believe if nothing is done this species will be extinct within 10 years," Schuster said.

While measures such as isolation, culling, or vaccination typically help for curbing some infectious diseases, Schuster explained, the facial tumor disease is already so widespread that it may be too late for such strategies.

As such, researchers are working on captive breeding programs for the animals and doing research into the disease and its spread — including studies that rely on genomic approaches for looking at everything from the genetics of the cancer itself to the genetic diversity present within remaining devil populations.

Last fall, researchers from the Wellcome Trust Sanger Institute and Illumina announced that they had sequenced the genome of a Tasmanian devil and a pair of facial tumor genomes using the Illumina HiSeq 2000.

For the latest study, Schuster and his co-workers relied on the Roche 454 Titanium platform and the GS FLX Titanium XL, a longer read platform that was used through an early access program.

The team sequenced the genomes of two Tasmanian devils — a devil known as Cedric who survived initial exposures to the facial tumor disease and another, called Spirit, who did not.

After building a reference genome based on their Titanium and Titanium XL+ data, the team then overlaid additional sequence data that they'd generated with the Illumina GAII before looking for informative SNPs — variants that can eventually be applied to genotyping arrays for tracking Tasmanian devil genetic diversity, population patterns, and more.

Because mitochondrial genome data from present day devils and museum specimens suggests genetic diversity has not declined over the past 130 years, Schuster said, it should be feasible to maintain the existing genetic diversity through breeding programs.

Even so, Schuster argues that such programs would benefit from genetic insights. For instance, with mitochondrial marker data pointing to five Tasmanian devil haplogroups, he said, it may be useful to know which genetic sub-population an animal belongs to before including it in a particular breeding pool.

Based on their data so far, Schuster noted, it appears that fewer than 10 devils would be needed for effective insurance breeding programs if the ideal combination of animals was chosen.