Assembly whale done

Pygmy sperm whales (Kogia breviceps) are named after a waxy substance known as spermaceti found in their heads. It is this oil sac that helps the whales focus sound.

Pygmy sperm whale (Kogia breviceps); Rescued in accordance with NOAA's Marine Mammal Health and Stranding Response Program MMHSRP Permit #18786-04

Pygmy sperm whales are found in temperate and tropical seas worldwide but are most commonly found off coasts and along continental shelves. These mammals are often confused with their closest relatives known as dwarf sperm whales (Kogia sima). In fact, they were not distinguished as separate species until 1966. [1]

These gentle creatures are often seen either alone or in small groups of six to eleven individuals. They spend little time at the water’s surface, only when the sea and weather conditions are very calm, and almost never approach vessels. When spotted, they are usually swimming slowly or lying still (behavior commonly referred to as “logging”). While they do have a blowhole, they do not have a visible blow at the surface.

Pygmy sperm whales do not face the threat of direct hunting, but are affected by entanglement in nets and ingestion of marine pollution. As the species avoid vessels and planes, scientists rarely see pygmy sperm whales at sea. This makes it difficult to estimate their population size or current population trends. [2]

Today, we share a chromosome-length genome assembly for the pygmy sperm whale based on a draft published by the Zoonomia Project (Genereux et al., 2021). The draft was scaffolded to 21 chromosomes using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details. The interactive contact map of the pygmy sperm whale’s chromosomes is included below:

We gratefully acknowledge SeaWorld for providing the sample for this work and special thanks to Lexi Mena for help with the photo and sample coordination. As always, we thank the Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support of the upgrade.

Blog by: Ashling Charles and Parwinder Kaur

Marsupial cats of Australia

The eastern quoll (Dasyurus viverrinus), formerly known as the eastern native cat is a medium-sized carnivorous marsupial found only in Australia. It is one of six extant species of quolls.

Eastern quoll, photo by Edwinna Bartley [CC BY-NC 2.0], via flickr.com

The size of a small domestic cat, it’s no wonder the eastern quoll is a favourite marsupial of those lucky enough to see one. Nocturnal by nature, this solitary but bold carnivore usually hunts in open country or woodland. It can occasionally be spotted foraging by day but prefers to spend daylight hours in nests made under rocks in underground burrows or fallen logs.

Eastern quolls are generally about the size of a small domestic cat. Females are significantly smaller, measuring 48 to 58 cm (19 to 23 in), and weighing around 0.7 kg (1.5 lb). The eastern quoll has a pointed nose, and a bushy tail. They have a thick coat covered by white spots, that can be either light fawn or near black, with off-white underparts stretching from the chin to the underside of the tail. Eastern quolls can be distinguished from all other species of quoll by the presence of only four toes (rather than five) on the hind feet, lacking the hallux (1).

The species is currently classified as Endangered by the IUCN Red List of Threatened Species (2). It is functionally extinct on mainland Australia due to disease and predation by introduced predators (red fox and feral cat), but remains widespread in Tasmania, and is also found today on Bruny Island. The lack of foxes in Tasmania likely has contributed to the survival of the species there; however, unseasonal weather events and predation by feral cats are thought to be contributing to a possible recent decline in the Tasmanian population.

Today, we share the chromosome-length genome assembly for the eastern quoll. As far as we know, this is the first whole-genome resource for the species. This is a $1K genome assembly, with contig N50 of 42kb and scaffold N50 of 531Mb. See our Methods page for more detail on the procedure. The interactive contact map of the eastern quoll’s chromosomes is included below.

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.

We hope that this assembly will provide the genomics resource towards the Tasmanian Quoll Conservation Program (TQCP), to estimate the genome-wide genetic diversity present in the existing Tasmanian population, ensure mainland populations being released in wild and otherwise help protect this charismatic marsupial cat.

Citations

1. Jones, M.E. & Rose, R.K. (2001). "Dasyurus viverrinus". Mammalian Species. 677: 1–9. https://doi.org/10.1644/1545-1410(2001)677<0001:DV>2.0.CO;2

2. Burbidge, A.A. & Woinarski, J. (2016). Dasyurus viverrinus. The IUCN Red List of Threatened Species 2016: e.T6296A21947190. https://dx.doi.org/10.2305/IUCN.UK.2016-1.RLTS.T6296A21947190.en

Fin-al fantasy

Next to the blue whale, the fin whale is the second-largest mammal in the world. Unlike blue whales, fin whales have pointed heads and streamline bodies, allowing them to move quickly in the water.

Photo Description - Fin Whale (Balaenoptera physalus) Photo Credit – Chris Buelow from Massachusetts, United States, CC BY-NC 2.0, via Creative Commons

Each whale can consume up to 1800 kg of food in a day. Fin whales belong to the baleen whale family and as such their diet tends to include krill, plankton, small fish and occasionally squid. Fin whales in the Southern Hemisphere appear to have an overwhelming preference for krill, which puts them into competition with other baleen whales in the Antarctic region. As a unique feeding technique, fin whales have been observed to herd schools of fish into dense clusters by circling at high speeds before engulfing the ball of fish whole. Talk about being efficient!

Fin whales are typically found alone, but occasionally form groups of less than ten. Like blue whales, fin whales communicate through vocalizations.

In the early days of whaling, fin whales were almost completely immune from whalers because of their speed and preference for cold, open ocean, although they were occasionally hunted in small numbers. However, as other slower, more unfortunate whales were depleted and faster steam-powered boats came into existence, fin whales became a new target for whaling. Fin whales were hunted in large numbers up until 1975, and as a result are now classified as a vulnerable species. Today, the biggest threats to fin whales are fast-moving ships. Collisions with ships injure these whales, leaving them stranded. The increase of ocean noise due to ships also impedes recovery of the fin whale populations as this noise hinders communication between male and female whales, making it difficult to find a mate.

The genome assembly scaffolded to 22 chromosomes shared today was generated using the muscle sample provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center generates research findings and scientific outputs at volumes similar to top academic institutions. In addition, the Center serves as a resource and thought leader in animal care, education and scientific communities.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

We thank Barbie Halaska and Ben Neely for their help with this genome assembly!

Learn more about the impact of The Marine Mammal Center’s scientific research and fin whales by visiting the Center’s website at MarineMammalCenter.org.

This is a $1K genome assembly. See our Methods page for more details on the procedure. We gratefully acknowledge Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support for this genome assembly.

Check out the interactive contact map of the 22 chromosomes of the fin whale below. For more information, details and data including the draft and the chromosome-length fastas and the mitochondrion sequence please visit the corresponding assembly page!

Blog by: Daniel Lim, Parwinder Kaur, Barbie Halaska and Giancarlo Rulli