DNA Zoo Blog

This blog aims to shout out the release of new assemblies and sharing of data on this website.

For the Rough-toothed dolphin, Steno bredanensis, group travel is the way to go! One of the smaller and less understood members of the Delphinidae family, rough-toothed dolphins are a generally social species that travels in tight-knit pods of 10-20 individuals. Rough-toothed dolphins are known to often associate with other cetacean species, including bottlenose dolphins, pantropical spotted dolphins, short-finned pilot whales, and spinner dolphins. The species is found throughout the world and most often frequents deep warm tropical waters and warmer temperate waters. [1].

Rough-toothed dolphins most common exterior characteristics are their dark gray bodies with distinct white throat and "lips". They also have a narrow dark cape patterned feature between the blowhole and dorsal fin. The animal’s underside is typically distinguished by some white, lighter spots, or blotches. [2].

Boasting a unique “reptilian” appearance that is atypical among their Delphinidae family counterparts, rough-toothed dolphins have a small head with a long beak. The species does not have any real feature separation between their sloping melon (forehead) and beak either. Their dorsal fin and flippers are quite long. [3].

Steno bredanensis by Gustavo Perez, [CC-BY-SA-3.0], via wikimedia.org

Today we share the chromosome-length genome assembly for the rough-toothed dolphin. This is a $1K genome assembly with a scaffold n50 = 95 Mb and a contig n50 = 60 Kb. For assembly procedure details, please see Dudchenko et al., (2018).

The sample for this genome assembly was provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center generates research findings and scientific outputs at volumes similar to top academic institutions. In addition, the Center serves as a resource and thought leader in animal care, education and scientific communities.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

Want to compare this Rough-toothed Dolphin genome against other members of the Delphinidae family? You’re in luck as this is the DNAZoo’s 9th genome assembly of a dolphin species! Check out, e.g. the assembly pages for the bottlenose dolphin and the Risso’s dolphin.

We thank Barbie Halaska and Ben Neely for their help with this genome assembly!

Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the Center’s website at MarineMammalCenter.org.

The dingo is Australia’s wild canid and is the continent’s iconic top-order predator. Dingoes arrived in Australia approximately 5,000 years ago and since then have become an integral part of the Australian ecosystem and culture (1). Aboriginal Australians shared a close relationship with dingoes and frequently featured them in their dreamtime stories and cave paintings (2). Today, many pure dingoes live in the wild, independent of human interference. Others live in symbiosis with native Aboriginal Australians as camp dogs.

Dingoes are distributed across most of Australia – from snow-covered alps to open barren deserts, from grasslands to the lush rainforests. Eye-catching but like many predators can be dangerous. They are generalist predators and commonly hunt rabbits, feral pigs, rodents, lizards, and even kangaroos and thus are essential to maintain ecological balance (3). Dingoes have been known on occasion to hunt farm animals, making them unpopular with some farmers. They are known to breed with domestic dogs and produce hybrids (4).

Sandy - the desert dingo; Photo: Barry Eggleton.

Dingoes inhabit a wide range of environments and climatic zones spanning the entirety of Australia. Based on their habitat they have been reported to differ in their morphology, physical appearance, body stature and several skeletal measurements (5). These differences lead to the inference that there may be three ecotypes or subspecies of dingo - Alpine, Desert and Tropical (6). However growing pile of evidence indicate the presence of only two subgroupings- Alpine and Desert.

Desert dingoes inhabiting the central Australian desert are usually smaller than Alpine dingoes. Here we release a chromosome-length genome assembly of the wild-born Desert dingo – Sandy (Version 2). Sandy was found as three-week old pup in the central Australian desert in 2014. Based on genetic testing, Sandy is identified as a pure Desert dingo. Version 1 of the assembly was enabled by winning the PacBio 2017 “World’s most interesting genome” competition. Thank you to Pure Dingo for providing the sample for this assembly. The genome will provide a better understanding of the genes that influence the transition from wild animal to domestic animal.

This assembly has a contig N50 = 40,716,615bp and scaffold N50 = 64,250,934bp, and is now available on NCBI as ASM325472v2. See the interactive Hi-C contact for the final assembly below!

The dingo is the Australian canine, which is thought to be introduced to Australia by seafarers from Asia around 5000 year ago (1). Since then the dingo has become Australia’s apex predator on land and has integrated into local ecosystem. By controlling populations of native and introduced herbivores including introduced mesopredators such as red foxes and cats, dingoes are fundamental for maintaining balance in the ecosystem. Additionally, by controlling populations of herbivores, dingoes benefit plant communities and other smaller native prey such as small marsupials and rodents (2).

Cooinda the Alpine dingo; Photo: Bargo Dingo Sanctuary.

The dingo is a medium-sized canine, with males being slightly larger than females. The dingo breeds once a year and usually produces a litter of four to six pups. The dingo may have multiple coat colours: ginger with white feet, darker tan to black, white, and golden yellow. Interestingly, like wolves, dingoes howl to communicate. The extensive hybridisation with domestic dogs has raised concerns over the persistence of pure dingoes in the wild.

Morphological and genetic studies have indicated a subgrouping in dingoes – Desert, Alpine and Tropical, primarily based on their geographical distribution. Skull shape differ between dingoes from different climatic zones, where the skulls of dingoes from the southeastern alpine regions of Australia are wider than the skulls of dingoes from the northwestern desert parts of Australia (3). Genetic studies however have supported the presence of only two lineages: Desert and Alpine (4). Alpine dingoes are found in the high elevation Australian alps and grow a thicker fur during late autumn. Alpine dingoes are typically larger than desert dingoes (5).

Here we release a chromosome-length genome assembly of the Alpine dingo - Cooinda. Cooinda is a pure dingo and was raised in the Bargo dingo sanctuary. Unfortunately, she has now passed, but it is expected she will go on display at the Australia Museum, Sydney as the type representative of the Alpine dingo. This assembly has a contig N50 = 23,108,747bp and scaffold N50 = 64,752,584bp. See Dudchenko et al., 2018 for details on the procedure. Thank you to Bargo Dingo Sanctuary for providing the sample for this assembly.

The assembly is now available on NCBI as UNSW_AlpineDingo_1.0:


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