• Ruqayya Khan

The South American tapir, Tapirus terrestris, is the largest surviving native terrestrial mammal in the Amazon. Although tapirs are physically similar to pigs, they are actually an odd-toed ungulate that's more closely related to horses and rhinoceroses [1]. South American tapirs primarily forage and consume vegetation native to the Amazon, including fruits like the mombin and the huito [2].


As in other tapir species, the South American tapir's nose and upper lip combine into a flexible snout like an elephant's trunk. The elongated nose is not just for show! The tapir makes up for their relatively poor eyesight with their strong sense of smell, helping them to locate food and potential mates. Their trunks are also prehensile, meaning they're able to grip tree branches to clear off fruit and leaves.

The ICUN categorizes the South American tapir as vulnerable with its population in declining trend. The biggest threats to the South American tapir are similar to many Amazonian species: habitat loss to logging and poaching their meat and hides [3]. Natural predators of the tapir are jaguars and crocodiles. In a threatening situation, tapirs may emit a high pitched squealing noise. Additionally, tapirs are great swimmers and may escape from predators by swimming away while using their magnificent snouts as snorkels [4].

South American Tapir (Tapirus terrestris) by Allan Hopkins, [CC BY-NC-ND 2.0], via flickr.com

Today we share the chromosome-length assembly for the South American tapir. This is a $1K genome assembly with contig N50 = 46 Kb and scaffold N50 = 47 Mb (see Dudchenko et al., 2018 for procedure details). The genome was generated using a sample from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center stored all the way back in 1977! We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample.

This is the second tapir species in our collection of genome assemblies (out of four recognized extant species of tapir). Check out this blog post and assembly page for the Malayan tapir, the only Old-World species of tapir. Interestingly, the species are hugely different in terms of karyotype: the Malayan tapir has a karyotype of 2n=52 whereas the South American Tapir has a karyotype of 2n=80! Check out the whole genome alignment plot below to find all the chromosomal breaks between the two.

Whole-genome alignment plot between Tapirus_terrestris_HiC and Tapirus_indicus_HiC

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:


Basenji’s are an ancient dog breed, originally indigenous to central Africa. Basenji-like dogs are depicted in drawings and models dating back to the Twelfth Dynasty of Egypt [1] and they sit at the base of the currently accepted dog phylogeny [2]. Basenjis share many unique traits with pariah dog types. Like dingoes and New Guinea Singing dogs (NGSD), Basenji’s come into oestrus annually—as compared to most other dog breeds, which have two or more breeding seasons every year. The annual oestrus of Basenji is possibly an adaptive response to protect puppies from higher temperature and humidity of the equatorial summer. In the rainforests the key factor affecting breeding is the availability of food [5].

They are often referred as “barkless” dogs of Africa. Basenji, dingoes and NGSDs are prone to howls, yodels, and other vocalizations over the characteristic bark of modern dog breeds. One explanation for the unusual vocalisation of the Basenji is that the larynx is flattened [3]. Basenji’s have short, fine chestnut red and black coat colour with white feet, chest and tail tip.

China striking a pose; Photo: Zanzipow Kennels

The Basenji made its debut in the western world in 1895 when a brace of the dogs was exhibited at the Cruft's show as African Bush dogs or Congo Terriers. Unfortunately, all contracted distemper shortly afterward and died. In England, the breed traces back to six dogs that were transported from Africa by Mrs. Olivia Burn in the 1930’s. The dogs were passed as pure breed by Kennel Club and zoological experts, and placed into the hound group.


Prior to 1987, a total of 28 Basenjis were exported directly from Africa to Europe or the United States [4]. Most of the imports went to England. Six were imported to the United States including one that came as a stowaway in a coffee shipment and two that came with a shipment of baby gorillas. In the 1970s and in the 1980s five Basenjis were imported into Germany. Subsequently, the American Kennel Club re-opened its stud book on multiple occasions so that additional Basenji’s from Africa could increase the genetic diversity of the breed.

Here we release a chromosome-length genome assembly of the Basenji – China or more formally Australian Supreme Champion Zanzipow Bowies China Girl. The genome assembly (Oxford Nanopore + BGISEQ + Illumina Hi-C) is of high quality with the contig N50 of 23,108,747 Mb and scaffold N50 of 64,752,584 Mb. See Dudchenko et al., 2018 for details on the procedure. Thank you to Jennifer Power for providing the sample for this assembly.


The genome is now available on NCBI as UNSW_CanFamBas_1.0:

References:

1. Dollman, G. The Basenji Dog. Journal of the Royal Africa Society 36, 148-149 (1937)

2. Parker, H. G. et al. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development. Cell Rep 19, 697-708 (2017)

3. Ashdown, R. R. & Lea, T. The larynx of the Basenji dog. J Small Anim Pract 20, 675-679 (1979)

4. America, B. C. o. Foundation stock sorted by year of import, 2017)

5. Johannes, J. E. (2003). The Basenji Annual Estrus: The impact of the rainforest ecology on its development.

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