All’s whale that ends whale

The gray whale, Eschrichtius robustus, is a member of the baleen whale family. Their name comes from their mottled skin with gray and white patches, due to being covered in barnacles, whale lice, and other parasites. (Actually barnacles may have a mutualistic relationship with their host whales, providing protection from attack from killer whales [1].) Female gray whales are usually larger than males, reaching sizes of approximately 14.9 meters, and weighing up to 41 tonnes [2].

Gray whales have the longest annual migration of any mammal, making 10,000-12,000-mile round trips around the North Pacific Ocean. During their migration, gray whales stick close to the shores, preferring shallower waters [3]. Their close proximity to land and their natural curiosity cause them to be frequently spotted by whale watching tours.

Gray whale breaching by Eric Neitzel, [CC BY-NC-ND 2.0], via flickr.com

Once at the brink of extinction in the early 1800’s, conservation efforts and hunting bans have allowed the eastern population of gray whales to return to pre-whaling levels! In 1994, gray whales were officially removed from the endangered species list, though the Western North Pacific population is still endangered [5]. All gray whales are still protected under the MMPA! As whales play a large role in the oceans’ ecosystems, preserving the gray whale species will have boundless effects on other marine life.

Today we share the chromosome length assembly of the gray whale, with contig N50 = 67Kb and scaffold N50 = 103 Mb. This is another $1K genome assembly, for procedure details, see Dudchenko et al., 2018. This is the third baleen whale (Mysticeti) in our collection so don’t forget to check out Bryde's whale and the North Atlantic right whale as well!

This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used in this study was collected by Pam Tuomi (Alaska Sealife Center) from Girdwood, Alaska and provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, and which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project.

Post by: Ruqayya Khan and Ben Neely

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).