The panda dolphin

The Commerson’s dolphin (Cephalorhynchus commersonii) aka skunk dolphin aka panda dolphin is best known for its distinctive, black and white body that consists of black fins, flippers and head, with white covering all other regions. These dolphins are small in size and found largely across the southwest Atlantic Ocean, with some populations also seen in the Indian Ocean. Other than their vastly different geographic habitats, Commerson’s dolphins found in the Indian Ocean also differ physically from their Atlantic counterparts. The dolphins seen in the Indian Ocean tend to have more grey patterns along their body and are also usually larger in size. [1]

Given their small size, these dolphins are extremely agile and register swimming speeds as fast as 11 to 13 kmph, often seeing riding waves surrounding high-speed boats. They are friendly to other relatives and like to associate with the Peale’s dolphin (Lagenorhynchus australis) when performing spectacular acrobats and playful swimming routines!

Photograph by GP0STRFPH, Greenpeace UK [CC BY 2.0], via flickr.com

Typically, Commerson’s dolphins exist in groups of 2-3 individuals but are also known to travel and socialize in groups as big as 100 individuals. Although their life spans in the wild average at around 10 years of age, one captive individual at SeaWorld (San Diego) lived for a record-breaking 25.8 years! Previously, these dolphins were often intentionally captured by fishermen for use as bait, but the practice has since been outlawed, allowing populations level to rise again. Yet, accidental entanglement in fishing nets continues to be a threat to these dolphins. [2]

Today we release a chromosome-length assembly for the Commerson’s dolphin species, our seventh assembly in the Delphinidae (oceanic dolphins) family (see our assemblies page here). This is a de novo assembly with contig N50 = 92Kb and scaffold N50 = 104Mb. See Dudchenko et. al, 2018 for details on the protocol. We thank SeaWorld for their help with the sample!

Back in Black

The black rhinoceros (Diceros bicornis) is the smaller of the two African rhinoceros species, but still stands just shy of 6ft tall at the shoulders. These mammals are not only massive, but quite fast. Weighing in at up to 1.5 tons, they can still reach a top speed of 34 mph while running on just their toes [1]!

As herbivores, the rhino intakes around 120 pounds of foliage, and does so by browsing on woody plants and shrubs [2]. They’re specially equipped with a notably pointed upper lip that’s used to pull the leaves off the branches and into their mouths.

The black rhinoceros sports two large horns on its head, in contrast to the white rhinoceros which bares only a single horn. In the wild these horns are used to ward off encroaching animals and defend territory. Large horns therefore are very desirable when searching for a mate.

"Black rhino" by Paul Albertella [CC BY 2.0], via flickr.com

Black rhino numbers once soared into the hundreds of thousands across sub-saharan Africa, but during the early 1990’s these numbers dwindled down to as low as 2,500 due to unregulated hunting and poaching [3]. This was an immense 98% drop in population. However, the numbers have been on the rise, with wild black rhinoceros population reaching more than 6,421 [4]. The IUCN lists these beautiful animals as critically endangered. Read more about these animals here.

Today, we release a chromosome-length genome assembly of the black rhinoceros. This is a $1K genome assembly with contig N50 = 87 Kb and scaffold N50 = 59 Mb. See Dudchenko et al., 2018 for details on the procedure. Thank you to SeaWorld for providing the sample for this assembly. This is the third rhinoceros in our collection, and completes the assembly of both African rhinoceros species, the other being the white rhinoceros (Ceratotherium simum). Additionally, we have previously shared the assembly of the Indian rhinoceros (Rhinoceros unicorns).

A tail with a hoppy ending

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 flickr.com

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).