The Basenji dogs included in the study. a. China. Is registered asAustralian Kennel Club Supreme Champion Zanzipow Bowies China Girl. Herregistration is #2100018945. She was born in 2016 and she is free of all knowngenetic diseases. Her sire and dam are Australian bred and her most recentancestor from Africa was 18 generations ago. Photo credit: Dylan Edgar. b.Wags. Is registered as American Kennel Club Champion Kibushi the Oracle, bornin in 2008. His registration number is HP345321/01. His sire is an Americanbred dog while his dam was imported from the Haut-Ule district of the DRCCongo, 3°24′04.0″N 27°19′04.6″E, in 2006. Photo credit: Jon Curby

An international study led by UNSW researchers has mapped one of the mostintact and complete dog genomes ever generated.

The genome sequence of the Basenji dog ( Canis lupus familiaris ) could havea big impact on the understanding of dog evolution, domestication and caninegenetic diseases.

The Basenji – also known as the barkless dog – is an ancient African dog breedwhich still lives and hunts with tribesmen in the African Congo. In the study,published in BMC Genomics, the researchers say the genome of the Basenji,which sits at the base of the dog breed family tree, makes an excellentunbiased reference for future comparisons between dog breeds and evolutionaryanalysis of dogs.

“The dog was probably the first animal to be domesticated by humans and hassubsequently been artificially selected by humans into a great diversity ofdog breeds of different sizes and shapes,” lead author of the study and seniorlecturer in Genomics and Bioinformatics at UNSW Sydney’s School ofBiotechnology and Biomolecular Sciences, Dr Richard Edwards says.

“Before this paper, it was difficult to interpret differences between the dogreference genomes and non-domesticated dogs, such as dingoes, jackals,coyotes, wolves and foxes. Big changes could be the result of recentartificial selection during creation of the specific reference breed. Byadding such a high-quality genome at the base of the domestic dog family tree,we have provided an anchor point for studies that can help establish thetiming and direction of genetic changes during domestication and subsequentbreeding.”

Dr Edwards says the Basenji genome sequence is different to the traditionaldog reference genome, CanFam, which is of a highly-derived breed, the Boxer.He says the choice of dog reference genome can affect the results of futuredog genetics studies looking at genetic variants. “For example, the Boxer ismuch more closely related to other Mastiffs than other breeds,” he says. “Thismay introduce biases in genetic analyses across many dog breeds. There is alsothe risk that breed-specific variation may map poorly – or not at all – to abiased reference. In principle, the Basenji is equally distant from mostmodern breeds, making it a less biased basis for comparisons.”

Dr Kylie Cairns is an expert in dingo identity and evolution in the Centre forEcosystem Science in UNSW’s School of Biological, Earth and EnvironmentalSciences. She says the Basenji genome now provides a high-quality comparisonto all domestic dog breeds for future studies. “As Basenjis are a very oldbreed, they provide the perfect comparison to more modern breeds to explorehow breeds were developed, the process of domestication and assist in studieslooking for disease genes,” Dr Cairns says. “This genome will also be criticalin comparisons to wolves, dingoes and village dogs as an example of an ancientdomestic breed.”

She says the Basenji genome may allow scientists to more fully unravel theevolutionary history of early dogs and how humans have shaped the first dogsinto the companions and breeds we have today.

“Many people wouldn’t realise that most dog breeds arose in the last 200-300years,” she says. “So having access to a high quality refence genome from anancient breed such as the Basenji gives insight into early breed developmentand how domestic dogs have been shaped by humans in the last few thousandyears.

“We will also be able to tackle lingering questions about the evolutionaryhistory of dingoes and their relatives in New Guinea, with the Basenji actingas a halfway point between non-domesticated dingoes and truly modern dogbreeds like pugs, kelpies and poodles.”

Dr Edwards says the genome of the Basenji is one of only a handful ofreferenced quality genomes for specific dog breeds. The first of these was aGerman Shepherd, Nala, which Dr Edwards also contributed to last year. DrEdwards says researchers combined three cutting edge genome sequencingtechnologies to assembly the Basenji dog genome, which is based on a femaledog called China. “Over 99% of the final genome assembly can be found in the39 pieces that represent the 39 dog chromosomes,” he says. “These chromosomesonly have one hundred regions of unresolved sequence, which is the fewest ofany published dog genome so far. This makes it one of the highest-quality doggenomes produced to date.”

The study also features a number of interesting genome assembly case studiesthat demonstrate the importance of curation and careful analysis, even forhigh-quality genomes. “Even the best technologies can still make mistakes,” DrEdwards says.

For example, the mitochondrial genome – a separate, small genome belonging tothe cell’s energy generators – had mistakenly been assembled into the middleof one of the chromosomes at one stage.
“Genomics has a come a long way in recent years, but we’ve not reachedperfection yet. At the same time, it is not possible to manually scan over twobillion DNA letters for mistakes. Part of what drives the research in my labis finding improved ways to use computers to help identify and fix theseerrors.”

Read the study in BMC Genomics.

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