Always spotted but rarely seen

Meet the largest living fish in the ocean, the whale shark (Rhincodon typus) growing up to 12 metres long! Whale shark is the sole member of the genus Rhincodon and the only extant member of the family Rhincodontidae. The name "whale shark" refers to the fish's size, being as large as some species of whales.

Photo Description: The whale shark (Rhincodon typus). Photo Credits – Australian Institute of Marine Sciences (AIMS), [CC BY 2.0]

Whale sharks are covered in a pattern of spots that is unique to each shark, much like human fingerprints. Inside their roughly 1.5m-wide mouths, they have over 300 rows of tiny teeth. Despite this impressive dental array, these fish are filter feeders, swimming forward to swallow prey. They eat krill, crab and fish larvae, small schooling fish, and jellyfish. Humans are not on the menu. Whale sharks are docile creatures, often allowing humans to swim near them.

Whale sharks live in warm and tropical seas and are highly migratory animals that swim across vast ocean distances, often diving to depths of more than 1,000 metres below the surface to feed and thermoregulate. Feeding aggregations occur seasonally at several locations, including Ningaloo Reef in Western Australia, where they support a tourism industry worth over twenty million dollars.

The whale shark is ovoviparous, meaning the female produces eggs that hatch insider her. When the young are fully developed, the female gives birth to around 300 live young. Whale sharks reach sexual maturity at 30 years and live to a total of around 70 to 100 years.

The whale shark is listed as endangered (population trend decreasing) on the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species. Key risks are vessel strikes and being caught accidentally by commercial fishing vessels.

The chromosome-length assembly we share today is based on the draft assembly published by Jessica Weber, Jong Bhak, George M. Church and coauthors in PNAS (Weber et al., 2020). This draft assembly was scaffolded with 279,901,000 PE Hi-C reads generated by DNA Zoo Australia labs and analysed using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

We gratefully acknowledge the tissue samples provided by Dr Luke Thomas from the Australian Institute of Marine Science (AIMS). The Hi-C work was supported 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 with funding from the Australian Government and the Government of Western Australia.

Check the interactive chromosome-length contact map below and a whole-genome alignment map to another shark genome in our collection, a chromosome-length upgrade for brownbanded bamboo shark Chiloscyllium punctatum from the draft published by Hara et al., 2018. Explore more details on the corresponding assembly page!

Whole-genome alignment plot between the new whale shark genome assembly (RhiTyp_1.0_HiC) and the brownbanded banboo shark genome assembly (Cpunctatum_v1.0_HiC) suggesting a high degree of karyotype conservation between species of carpet sharks (Orectolobiformes).

Citations:

1. Jessica A. Weber, Seung Gu Park, Victor Luria, et al., (2020) “The whale shark genome reveals how genomic and physiological properties scale with body size,” PNAS, 117 (34) 20662-20671; DOI: 10.1073/pnas.1922576117

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.

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.