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!

It takes one to snow one

From the Himalayas to the southern Siberian mountain range, the snow leopard (Panthera uncia) can be found on the prowl for its next meal. Snow leopards are no strangers to harsh terrains, travelling anywhere from 48 to 80 square miles [1]. These powerful predators can jump up to 50ft and can take down prey three times its own size [2]!

Young snow leopard by Tambako The Jaguar, [CC BY-ND 2.0], via flickr.com

To survive and blend in with snowy, mountainous environments, snow leopards have large paws that act as natural snowshoes and thick fur coats to protect them from harsh conditions. Their light-colored coats have dark rosette patterns that are unique to each individual [3]. Unfortunately, their beautiful coats are sought after by poachers. The IUCN lists the snow leopard as vulnerable, with their wild population in decline. Other threats to snow leopard populations include habitat loss and climate change.

Today, we share the chromosome-length assembly for the snow leopard, thanks to Kiara from the Oklahoma City Zoo. Before she passed in late 2017, she provided the sample for this genome assembly allowing for her genome to live on indefinitely. We thank the Oklahoma City Zoo staff and especially Candice Rennels and Jennifer D'Agostino for their help with this sample!

This is a $1K genome assembly with contig N50 = 65 Kb and scaffold N50 = 141 Mb. See Dudchenko et al., 2018 for procedure details. This is the fifth species in the DNA Zoo collection from the Pantherinae subfamily of cats, the others being the tiger, jaguar, leopard, and the clouded leopard. Stay tuned for more!