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Dingo Genome Progress Presented at PAG

SAN DIEGO (GenomeWeb) – A University of New South Wales-led team has sequenced and assembled a desert dingo genome de novo in the hopes of untangling canine domestication in general, along with the dingo's own history in Australia.

UNSW biotechnology and biomedical sciences researcher Bill Ballard presented the work during a PacBio workshop at the Plant and Animal Genome conference here yesterday. He noted that the research follows from pioneering work by the late Alan Wilton, a geneticist at the UNSW, who established a large dingo DNA repository.

The new genome-sequencing project is co-led by the University of Sydney's Claire Wade and won last year's SMRT Grant program. It focuses on a desert dingo named Sandy — found stranded with two of her siblings in a remote region in the state of South Australia when she was just a few weeks old.

For the de novo dingo genome sequencing effort, the team began by sending genomic DNA from Sandy's blood and skin biopsy samples to the Arizona Genomics Institute for PacBio long read sequencing. The resulting reads, including more than 150 billion bases of raw sequence data, were then put together de novo using the Falcon assembly tool by the molecular data analysis firm Computomics in Germany.

From there, the researchers added in 10X Genomics Chromium linked reads to scaffold the reads, followed by Bionano Genomics Irys mapping to do further scaffolding and establish super scaffolds.

In the process, they were able to whittle down the contigs and incrementally ratchet up the contigN50 of the assembly, landing on a dingo genome that is 2.4 billion bases long and spans some 98 percent of the CanFam3.1 domestic dog reference genome, which was used for preliminary analyses of the new dingo sequence.

The original version of the domestic dog reference, representing a female Boxer named Tasha, appeared in Nature in 2005. During a PAG session on Sunday, University of Bern genetics researcher Vidhya Jagannathan outlined ongoing efforts to re-assemble Tasha's genome with new sequence data, as part of the Dog 10K Genomes project.

The dingo sequencing team is also pursuing new domestic dog (and wolf) sequences for the ongoing analyses: The group reportedly plans to compare Sandy's genome to grey wolf and German Shepherd genomes that are sequenced using a combination of low-coverage PacBio sequencing, 10X Genomics reads, and Bionano Genomics mapping. It is also generating transcriptomic sequences from a captive alpine dingo to aid in their genome annotation efforts.

Ballard explained that the dog-dingo-grey wolf comparison is expected to offer clues to canine domestication, while perhaps providing a more detailed look at the dingo's introduction to Australia.

It is largely believed that dingoes reached the continent some 5,000 to 8,000 years ago, he explained. But that estimate is complicated by conflicting evidence, including a more ancient cave painting that depicts a dingo-like creature.

Similarly, the animal's current place in Australia's landscape is hotly debated. Some see an iconic carnivore, Ballard said, others a sheep-killing scourge. Further complicating genetic and other studies of the dingo, he noted that there is frequent hybridization between dingoes and domestic dogs, making it non-trivial to find authentic representatives of the wild dog.

Still, there is evidence that the dingo itself is not domesticated. Its genome appears to contain just one copy of the amylase gene, for example. That gene has been duplicated in domestic dogs, presumably to help our canine companions more easily consume starchier foods they encountered while hanging out with humans.

Such evidence suggests dingoes "were never truly domesticated or alternatively they are a feralized domestic dog breed that has lost the duplication," Ballard wrote in an abstract accompanying the presentation.

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