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.

Potoroos in truffle

The critically endangered Gilbert's potoroo or Ngilkat (Potorous gilbertii) is believed to be Australia's rarest mammal and the world’s rarest marsupial.

Gilbert's potoroo is a small kangaroo-like marsupial in the family Potoroidae. It was first recorded for science in 1840 by the collector John Gilbert (hence the name). The few known historical records of the potoroo are all from the southwestern coast of Southwest Australia in 1843, 1866, 1869, and 1875, and the uncertain date of 1890s to the west. The species was believed to be extinct for over 100 years before it was rediscovered in 1994 in Two Peoples Bay Nature Reserve.

Photo Description – Gilbert's Potoroo or Ngilkat (Potorous gilbertii) Photo Courtesy – Dick Walker and GPAG

As soon as the species was rediscovered, it was recognised that the population was extremely vulnerable as it occurred in very long unburnt vegetation (60+ years) with high fuel loads and given its restricted distribution could be lost in a single fire.

For the past 25 years the Department of Biodiversity, Conservation and Attractions (DBCA) has undertaken a range of recovery actions including attempts at captive breeding and various types of assisted reproduction to establish a sufficiently large population of captive animals to use to create insurance populations in case the Two Peoples Bay population was lost. Unfortunately, due to Gilbert’s potoroo’s extremely specialist diet (over 90% hypogeal fungi, e.g. truffles, which makes it one of the most fungi-dependent mammals in the world) and possibly other genetic and behavioural characteristics, neither captive breeding nor any other assisted reproduction techniques were successful.

In 2005, DBCA and the Gilbert’s potoroo Recovery Team decided to abandon attempts at captive breeding and to focus instead on creating insurance populations at locations outside Two Peoples Bay. Ten animals were introduced to Bald Island east of Two Peoples Bay between 2005 and 2007 and into a 380-ha fenced enclosure at Waychinicup from 2010. In 2015 the long-predicted fire at Two Peoples Bay, ignited by a severe lightning storm, destroyed over 95% of Gilbert’s potoroo habitat leaving only about 5 survivors. A third safe haven population on Middle Island was created in 2018 to provide additional security for the species.

Gilbert’s potoroo is listed as Critically Endangered under the IUCN Red List, the Australian EPBC Act (1999) and the Western Australian Biodiversity Conservation Act (2016). The current population is estimated at about 100-120 individuals: Two Peoples Bay (about 3-5 animals), Bald Island (est. 70 animals), the Waychinicup enclosure (25 known animals) and Middle Island (10 translocated animals).

The long-term goal of the recovery program for Gilbert’s potoroo is to improve its conservation status by increasing both the size of existing populations and the number of populations. In order to do this, it is critical to understand the distribution of genetic diversity across the four sub-populations (wild and translocated) to inform population management strategies (including genetic augmentation or assisted gene flow) aimed at maximizing the retention of genetic diversity at the species level.

Today, we share the chromosome-length genome assembly for the Gilbert's potoroo. The assembly was generated using a sample from 2009 provided by Dr Tony Friend from DBCA. This is a $1K genome assembly, with contig N50 of 46kb and scaffold N50 of 558Mb. See our Methods page for more detail on the procedure.

The interactive contact map of the Gilbert's potoroo's chromosomes is included below, alongside the whole-genome alignment to another closely related marsupial from our collection, the tammar wallaby. Despite the close chromosome count, the whole-genome alignment suggests substantial interchromosomal rearrangements since the last common ancestor of the two species (estimated to have existed ~24 MYA). This is the first version of the genome assembly for the species ever. Since our first tackle at this, we've generated more data and hope to generate even more, so stay tuned!

The work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Illumina Inc., 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. The work was provided as an in-kind contribution to a Western Australian State Natural Resource Management Community Stewardship Grant awarded to the Gilbert's Potoroo Action Group, a volunteer community group seeking to help save Gilbert's potoroo.

Whole-genome alignment plot between the Gilbert's potoroo chromosome-length genome assembly (Potorous_gilbertii_HiC, 2n=12,13) and a closely related marsupial from our collection, the tammar wallaby (me-1k, 2n=16). Both genome assemblies are $1K genome assemblies.

We hope that this chromosome-length assembly will provide the genomics resource to assist in estimating the genome-wide genetic diversity present in the existing population as well as management of the species. We also hope that this data will enable research on genes involved in adaptation and disease, further increasing our ability to improve species resilience in the population management strategy. Working with the Gilbert's potoroo recovery team this resource will facilitate the integration of genetic information into conservation management for the species. We believe that creation of this genomic resource will have lasting benefits for the genetic management and long-term survival of this critically endangered species.

Join Gilbert’s Potoroo Action Group (GPAG), DNA Zoo Australia/University of Western Australia & Department of Biodiversity, Conservation & Attractions for an afternoon event Saturday September 4, 2021, 1:00pm - 4:00pm to unveil the genome puzzle for the world's rarest marsupial, Gilbert’s Potoroo, & learn about the importance of genetics for endangered species conservation. The genome will be launched by former WA Chief Scientist Prof Lyn Beazley & followed by a truffle-themed afternoon tea & time for discussion, socialising & participation in puzzles & activities.

Free event book here https://www.trybooking.com/events/landing?eid=798292&