Quollity genomic resource

The Northern quoll (Dasyurus hallucatus) is the smallest of the four Australian quoll species with adults weighing around 0.5-1 kg (males are larger than females). Northern quoll populations have declined by more than 75% since the introduction of poisonous cane toads, which the quolls mistake for food.

Photo Description: Northern Quoll (Dasyurus hallucatus). Photo credits: S J Bennett, CC BY-NC 2.0, via Creative Commons

The Northern quoll is a medium-sized carnivorous marsupial found in northern Australia. Northern quolls are relatively short-lived for an animal of their size, especially males which in the wild normally die soon after mating at only 1 year of age before their own offspring are born. During the mating season (around June to September), males expend considerable energy fighting other males, and do not survive to breed a second year. Females den in tree hollows, hollow logs and rock crevices; they raise a litter of up to eight young. At the end of the breeding season, the Northern quoll population is comprised almost entirely of mature females and their young. Females may live for two or three years.


Once widespread across northern Australia, the northern quoll now only occurs in fragmented populations and is classified as endangered by the IUCN. They reported to be critically endangered in the Northern Territory, and populations in Western Australia are vulnerable to extinction at very fast rates. The northern quoll's demise is attributed to several factors, including predation by invasive pests and habitat destruction, but more notably its predation on the toxic introduced cane toad. Several strategies are currently being investigated to combat the threat of cane toads, including targeted gene flow, training aversion behaviour, and engineering genetic resistance to the toad's toxin.

To support the above conservation efforts further, we share the first chromosome-length genome assembly for the northern quoll. This is a collaborative effort of DNA Zoo labs with Assoc. Prof. Ben Phillips and Dr Stephen Frankenberg from University of Melbourne along with Dr Adnan Moussalli from Museums Victoria. The chromosome-length assembly is based on a draft assembly produced using 10x Genomics Chromium linked-read sequencing of a male northern quoll fibroblast cell line, established from a tissue sample kindly provided by the Territory Wildlife Park, and assembled using Supernova with additional funding from the Hermon-Slade Foundation.


A liver sample from the same animal was used for the Hi-C sequencing. The 10X draft assembly was scaffolded with 722,045,107 PE Hi-C reads generated by DNA Zoo labs and processed 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 contact map of the Northern quoll’s 7 chromosome-length scaffolds below!

We hope that this assembly will provide a valuable genomics resource for northern quoll conservation, including the analysis of population genetics data and the development of genetic strategies to enable population recovery.


We gratefully acknowledge the resources provided by The University of Melbourne, Museums Victoria, The University of Western Australia and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre.