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

37 views0 comments

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

80 views0 comments

Updated: Oct 2

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

86 views0 comments