Sealing the deal on our 250th genome assembly

Gray seals (Halichoerus grypus) are sometimes called "horseheads" because of their large, curved noses. The male nose is so distinctive that the gray seal’s scientific name, Halichoerus grypus, means "hooked-nosed pig of the sea." (For those keeping track at home, “sea pig” is also the translation of porpoise.)

The gray seal is part of the "true" seal family, and does not have external ear flaps. The males can be quite large at up to 10 feet (3 m) long and weighing 880 pounds (400 kg). Though not as notorious for deep, long dives as Weddell seals or Elephant seals, the gray seal can dive to 1,560 feet (475 m) for as long as one hour. Gray seals breed on ice or sandy beaches in parts of Canada (Gulf of St. Lawrence, Sable Island, Nova Scotia) and on sandy or rocky beaches or islands in the U.S., and in parts of the Baltic Sea.

Credit: NOAA Fisheries/Kimberly Murray

Today, share the chromosome-length gray seal genome assembly! This is a $1K genome (cN50=62kb; sN50=141.6Mb), generated by the DNA Zoo team from short insert-size PCR-free DNA-Seq data using w2rap-contigger (Clavijo et al. 2017) (see Dudchenko et al., 2018 for details). The 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 (Field ID 07-486-Hg, Storage ID NM19K1111C) was collected from Gloucester, MA in 2008 by Belinda Rubenstein (New England Aquarium), and provided by the National Marine Mammal Tissue Bank, which is maintained in the Marine Environmental Specimen Bank (Marine ESB) at NIST, 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.

There are two pinnipeds in the US waters of the Atlantic throughout the year: the harbor and gray seals. Though nearly extinct in the 1960s, the gray seal population has rebounded to around 25,000 in US waters, with closer to 500,000 in nearby Canadian waters (NOAA Stock Report). The gray seal can be found on either side of the Atlantic, with three distinct populations: Northeast Atlantic, Northwest Atlantic and Baltic Sea, comprising two subspecies H. g. atlantica and H. g. balticus (Haug 2007; Boskovic 1996 and Olsen 2016). The sample used for genome assembly specifically came from the Western North Atlantic stock.

Check out how the 16 chromosomes of the gray seal fold inside the nucleus using the interactive Hi-C contact map of the assembled genome below. This genome is our 7th pinniped, after the spotted seal, harbor seal, bearded seal, Northern elephant seal, HA monk seal and the walrus, and marks our 250th genome assembly release. Yay!!! Stay tuned for hopefully many more to come.

Famously feisty

The Tasmanian devil (Sarcophilus harrisii), now listed as endangered, is a carnivorous marsupial. The size of a small dog, the Tasmanian devil became the largest carnivorous marsupial in the world following the extinction of the thylacine in 1936.

Tasmanian devil, photo by Mathias Appel [CC BY-NC 2.0], via flickr.com

Tasmanian devil is related to quolls, and distantly related to the thylacine. It is characterised by its stocky and muscular build, black fur, pungent odour, extremely loud and disturbing screech, keen sense of smell, and ferocity when feeding. The Tasmanian devil's large head and neck allow it to generate one of the strongest bites per unit body mass of any extant predatory land mammal. It hunts prey and scavenges on carrion.

Although devils are usually solitary, they sometimes eat and defecate together in a communal location. Despite its rotund appearance, it is capable of surprising speed and endurance, and can climb trees and swim across rivers. Devils are not monogamous. Males fight one another for females, and guard their partners to prevent female infidelity. Females can ovulate three times in as many weeks during the mating season, and 80% of two-year-old females are seen to be pregnant during the annual mating season.

Tasmanian Devils are wholly protected. They are listed as ‘endangered’ under Tasmania’s Threatened Species Protection Act 1995 (May 2008); the Commonwealth’s Environment Protection and Biodiversity Conservation Act 1999 (May 2009) and are placed on the Red List of the International Union for the Conservation of Nature and Natural Resources (2008).

Tasmanian devils declined in population over 3,000 years ago due to the introduction of the dingo, a pack animal that pushed the Tasmanian devil out of mainland Australia. Furthermore, in Tasmania, the island state that most Tasmanian devils currently call home, the animals are threatened by a transmissible, painful and fatal disease called Devil Facial Tumor Disease (DFTD) — one of only a few known contagious cancers — which decimated up to 90 percent of the wild population of Tasmanian devils. Habitat destruction adds yet another stress to the species’ persistence.

The chromosome-length assembly we share today is based on the draft assembly (Devil_ref v7.0 aka sarHar1) published by Elizabeth Murchison et al. back in 2012 (1). This draft assembly was scaffolded with 442,235,972 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details. Check out the interactive map below for the information on how the 7 chromosomes of the Tasmanian devil fold inside the nucleus based on the generated Hi-C data. Note that several more references for the Tasmanian devil are now available to the scientific community.

We gratefully acknowledge the tissue samples provided by the Ranger Red’s Zoo & Conservation Park and the collaboration with Natasha Tay, Harry Butler Institute, Murdoch University towards tissue preparations. The Hi-C work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre.

Citations:

1. Murchison et al 2012. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell. 2012 Feb 17;148(4):780-91. doi: 10.1016/j.cell.11.065.

A stellar Stenella

The species name for the Clymene dolphin, Stenella clymene, likely was inspired by the water nymph daughter of the Titan Oceanus, also named Clymene [1]. This dolphin species is also commonly known as the short-snouted spinner dolphin, not to be confused with the Eastern spinner dolphin whom they frequently school with. The Clymene dolphin is very "acrobatic", often spinning and jumping out of the Atlantic waters they call home [2].

Research done on mitochondrial and nuclear markers in Amaral et al. (2014) shows that the Clymene dolphin is likely the result of the natural species hybridization between two Stenella species, Stenella coerueloalba and Stenella longisrostris. In this paper, the authors note that the cranial features of the Clymene dolphin closely resemble those of S. coeruleoalba, but its external appearance and behavior are more similar to those of S. longirostris. Natural hybridization in mammals is believed to be rare event but also an opportunity to share beneficial mutations and increase genetic diversity.

There is still much to be learned about this species, including their reproductive habits and lifespan. Although not endangered, the Clymene dolphin is protected under the CITES Appendix II [3]. One of the main threats to this species is getting entangled in fishing gear and nets. Ocean noise made by industrial and military boats also disturbs the Clymene dolphin, which rely on sound and echolocation to hunt, communicate like many other marine mammals.

Clymene dolphins, photo by Keith Mullin [NOAA/SEFSC MMPA Permit 779-1633]

Today, we share the chromosome-length genome assembly for the Clymene dolphin, Stenella clymene. The genome was assembled following the $1K strategy described in (Dudchenko et al., 2018). See our Methods page for more details.

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 Clymene dolphin (Stenella clymene) specimen used in this study (Field ID WAM 602; Storage ID NM15K707C) was collected from from Topsail Island, NC by Bill McLellan (UNCW). This specimen was provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, 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.

This is the 4th Stenella dolphin species we've released so far. Check out the chromosome-length contact map for Stenella clymene below, and compare data to that released with the blog post by Ben Neely to learn more about other species in this fascinating genus of dolphins and compare their genome alignments! See also de novo assembly of the mitochondrion for the species shared in the full data release folder.