Why the long face?

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

It’s all in the family for the “reptilian” looking Rough-toothed dolphin

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.

Desert dingo from down-under

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!