March 5, 2018  |  Plant + animal biology

Dog meet dog world: Exploring canine genomes

UPDATE (October 2020):
Sandy’s genome assembly is now available here.

From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication. Intent on unraveling some of the developmental secrets of the process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain.
A desert dingo named Sandy has already provided some insight into the process after its genome was sequenced as part of the 2017 Plant and Animal SMRT Grant.
Study leader Bill Ballard described in this presentation at PAG 2018 that pure dingoes are intermediates between wild wolves and domestic dogs, with a range of domestication traits. This includes duplication of the amylase (AMY2B) locus, associated with adaptation to starch in the diet common in domestic canines, which the dingo lacked.
Being able to study structural variation was key, so Ballard was delighted to use SMRT Sequencing to generate a 60-fold coverage long read contig assembly. Working with program sponsors the Arizona Genomics Institute and Computomics (in Tübingen, Germany) and adding 10X Genomics Chromium linked-reads and Bionano Irys maps, his team was able to create a full 2.46 Gb assembly, with the longest scaffold reaching 123.2 Mb (spanning the entire chromosome 1 of the domestic dog genome).
His team is just beginning to delve into the data they generated from sequencing Sandy’s genome, but they have already noted differences in chromosomal loci. To fully annotate the dingo genome, they are also sequencing the transcriptome of three tissues and the epigenome.
The UNSW team will then compare the dingo genome with those of the grey wolf and the German Shepherd, which they also plan to generate with long reads. This will help shed further light on the domestication process.
Blood, saliva and hip x-rays have been collected from more than 400 German shepherds. They are hoping one dog in particular, Kira, will provide additional insight into a debilitating dog condition, hip dysplasia. The seven-year-old female has good hips, and her full DNA sequence could help identify why some dogs get the condition while others do not.
She has become the mascot of the project, and the poster dog for their Hip2Fit crowdfunding campaign. They are aiming to collect $50,000 AUS to cover the costs of PacBio sequencing and assembly and Bionano scaffolding.
“This work is critical to help ease the pain associated with this condition and to ensure that service dogs are able to help their humans for as long as possible,” Ballard notes on the fundraising page.
Identification of DNA variations that cause hip dysplasia in German Shepherds will also help future studies in other breeds that have hip-associated problems, including golden retrievers, St Bernards, labradors and rottweilers, he adds. Like the dingo project, it will also advance our overall knowledge of canine genetics and development.

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