Assembly updates

  • Ruqayya Khan

Updated: 13 hours ago

The brush rabbit, Sylvilagus bachmani, is one of several species of cottontail rabbits. They have a short, fluffy tails that may be white or gray in color. Inhabiting the western costal region of North America, brush rabbits may be found foraging through shrub-lands, woodlands, and coniferous forests. Though they rarely leave the brush for long, they may be seen basking in the sun in nice weather. If they’re feeling particularly excited or playful, brush rabbits can binky, jumping up in the air while twisting their bodies and kicking their feet [1]!

Brush rabbit by Allan Hack, [CC BY-ND 2.0], via

The brush rabbit are prolific breeders, producing around 3 litters with an average of four offspring a year [2]. The population is kept in check by their many predators, including snakes, foxes, coyotes, and bobcats. When startled, brush rabbits may thump their back feet on the ground in surprise! Brush rabbits avoid predators by running at speeds of 40 km/hr in zig zag patterns [3].  

Originally sampled in 1976, this assembly was created from primary fibroblasts obtained from T.C. Hsu CryoZoo at the University of Texas MD Anderson Cancer Center. 44 years later, we share the chromosome length assembly of the brush rabbit. This is a $1K genome assembly with contig N50 = 58 Kb and scaffold N50 = 116 Mb. See Dudchenko et al., 2018 for details on the procedure.

This is only a second chromosome-length genome assembly for a rabbit in our collection: previously we shared a few tweaks to the European rabbit genome assembly from the Broad institute (Lindblad-Toh et al., 2011), here. The second genome gives us the first opportunity to compare karyotypes within the rabbit family. Included below is the whole-genome alignment plot between the two rabbit genomes: the genome appear to be highly collinear, with two fusion events (circled in blue) apparent responsible for the difference in karyotypes: 2n=44 in the European rabbit vs 2n=48 in the brush rabbit!

Whole-genome alignment plot between the only other rabbit with a chromosome-length genome assembly before the brush rabbit, the European rabbit (assembly OryCu2.0_HiC, from the Broad institute with DNA Zoo tweaks) and the new brush rabbit genome assembly (Sylvilagus_bachmani_HiC).

  • Ren Larison

Mountain zebras (Equus zebra), endemic to South Africa and Namibia, are one of three extant species of extant zebras and comprise two recognized subspecies, the Cape mountain zebra (E. z. zebra) and Hartmann’s mountain zebra (E. z. hartmannae). Like their sister species, plains and Grevy’s zebras, they are recognizable by their iconic black and white stripes. Mountain zebras fall between the other two species in size and the thickness of their stripes. Mountain zebras can also easily be distinguished by the fact that they possess a dewlap, a fold of skin hanging from the throat.

As their name implies, they prefer mountainous terrain up to about 3000 feet. Once listed as endangered (IUCN Red List - 1996) with a global population of between 2-3000 only 80 of which were Cape mountain zebra, the species has rebounded to a global population of 35,000, 1700 being the Cape subspecies. They are still vulnerable, however, due to habitat fragmentation and the potential threat of increased drought due to climate change. It was drought that caused the catastrophic decline that led to the population nadir in the 1980’s.

Mountain Zebra stallion by Bernard Dupont, [CC BY-SA 2.0], via

Today we share the $1K assembly of the mountain zebra. The sample for the assembly was provided by a mountain zebra named Zakota and obtained by Greg Barsh (Hudson Alpha/ Stanford University) and Ren Larison (UCLA) during a visit to the Hearts and Hands Animal Rescue in Ramona, CA, owned by animal lover and zebra whisperer Nancy Nunke. During our visit Nancy had us stroke the fur along the back of a mountain zebra, allowing us to learn an unusual fact about them; the fur between the saddle and rump grows backward, with the nap back to front instead of front to back.

Like the plains zebra, the mountain zebra shows quite a bit of rearrangement in their chromosomes relative to the domestic horse (see whole genome alignment plots below). This rearrangement is also reflected in the large differences in number chromosomes among the three species, with the horse having 32 pairs of chromosomes, the plains zebra 22, and the mountain zebra only 16 – half that of the horse. In spite of these re-arrangements equids are notorious for their ability to hybridize, leading to the fascinating pelage patterns seen in hebras and zorses, as well as potential conservation threats due to hybridization between the rarer zebra species - mountain zebras and Grevy’s zebras - and the vastly more common plains zebra.

Whole-genome alignment between the new chromosome-length genome assembly for the mountain zebra (Equus_zebra_HiC) and that of the domestic horse (EquCab2.0, from Wade et al., Science 2009).

  • Ragini Mahajan

As the name suggests, the Asian Small-Clawed Otter (Aonyx cinereus) is the smallest of all otter species and inhabits parts of Asia, like Indonesia, southern India, China, and the Philippines. As semiaquatic mammals, they call rivers, streams, and even mangroves home. To facilitate life underwater, these otters are able to close both their nostrils and ears while swimming! [1]

Uniquely, Asian small-clawed otters use the webbing between their toes to locate and trap food instead of their mouths. Despite the small size of their paws, these otters are able to crush the shells of crabs and mollusks with their paws. When that isn’t possible, they cleverly wait for the heat from the sun to break open the shells and access the meat [2].

This is especially different from their otter relatives, like the Northern River Otter (Lontra canadensis), who exclusively capture prey using their mouths! (You can learn more about the Northern River Otter in a previous blog post.)

Photograph by Jen Zoon, Smithsonian’s National Zoo [CC BY-NC-ND 2.0], via

Asian small-clawed otters are heavily social, and typically exist in groups of 15-20 individuals. If you are ever around a family of these otters, you are likely to hear their many sounds, used for greeting, play, contact and alarm, as they are an extremely vocal species! Although this hasn’t been formally studied, many agree that they are incredibly otterable and very camera-friendly!

Sadly, Asian small-clawed otter populations have been slowly declining as a result of pollution, loss of habitat, and hunting. Which is why they are now considered a Vulnerable species by the International Union for Conservation of Nature (IUCN) [3]. Given that the biggest threat to their populations is loss of habitat and prey from pollution, there are simple things we can do to help this species. According to the Smithsonian, practicing the 3-Rs: Reduce, Reuse, Recycle (in that order), is an effective way of decreasing pollution and disturbance to the habitats of these Asian small-clawed otters. [4]

Today, we release the chromosome-length assembly for this otterly cute species. This is a de novo $1K genome assembly with contig N50 = 69 kb and scaffold N50 = 131 Mb. See Dudchenko et al., 2018 for details on the procedure.

For this genome assembly, we have used two samples from our collection. For DNA-Seq, the used blood donated by Hope, the small-clawed otter at the Houston Zoo. (Read more about Hope and her partner Danh Tu in this post by the Houston Zoo.) A blood donation from another otter, from San Antonio Zoo, was used to generate the Hi-C data for chromosome-length scaffolding. Thanks!


© 2018-2020 by the Aiden Lab.