Oh my cod

We’re excited to announce that Australia’s largest freshwater fish, the iconic Murray cod (Maccullochella peelii), has been added to DNA Zoo’s genomic database.

The Murray cod is one of Australia’s most iconic fish; a freshwater species that can grow to ∼1.8 metres in length, weigh more than 100 kilograms and live to ≥48 years old. This species is of conservation concern as it has undergone strong population contractions in the last century. It is also popular for recreational fishing and is of growing interest to the aquaculture industry.

Photo Description - Murray cod (Maccullochella peelii). Photo credits - Guo Chai Lim [CC BY-NC-ND 2.0], via flickr.com

The story of the Murray cod is not much different to that of most Australian endangered species. Due to its previous abundance, the cod was commercially fished from the early years of European arrival. Changes to its natural habitat and competition from introduced fish species have also had a big impact on Murray cod numbers declining.

The Murray cod inhabits the Murray-Darling Basin, which spreads through New South Wales, South Australia, Queensland, the Australian Capital Territory, and Victoria. Thousands of interconnected creeks and rivers run through the basin and below it you’ll find a complex system of aquifers and groundwater.

Also known as 'pigs of the waterways,' Murray cod are highly aggressive and territorial. They'll also eat almost anything that gets in their way; fish make up the majority of the diet of mature Murray cod, but they have also been known to eat ducks, cormorants, freshwater turtles, water dragons, snakes, mice and frogs.

The chromosome-length assembly we are releasing today is based on the draft assembly by Austin et al., 2017 generated using Illumina and Nanopore sequencing approach. This draft was scaffolded to 24 chromosomes with 20,178,257 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). You can find more details on our Methods page, and check out the interactive Hi-C contact map or the 24 chromosomes below!

The sample for Hi-C was kindly provided by David Carter and Dylan Skinns, CEO and General Manager of Sales and marketing respectively, from Austral Fisheries Pty Ltd. The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA), La Trobe University team with funding from the Australian Research Council (DE190100636). We gratefully acknowledge the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Murray cod, once listed as 'Critically Endangered' on the International Union for Conservation of Nature's Red List has been upgraded to 'Of Least Concern' as numbers increase. They're still however listed as 'Vulnerable' under the Environmental Protection of Biodiversity and Conservation Act. According to some estimates, cod numbers have been as low as 10% of those that existed before European settlement.

The cod has moved from being considered as a plentiful source of food to an important but threatened part of the Murray-Darling ecosystem. We hope the chromosome-length genome assembly resource for the Murray cod supports ongoing population genetics, conservation and management research; as well as assisting with better understanding the evolutionary ecology and history of the species.

Superb starling assembly

Superb starlings (Lamprotornis superbus) really are as impressive as their name suggests. Their shimmering, iridescent green and blue plumage makes them hard to miss on the African savanna.

Superb starling, photo by Dustin Rubenstein, Columbia University [CC]

Yet, what really makes them stand out from other birds is their complex social system. Superb starlings are plural cooperative breeders that form some of the largest and most complicated social groups of any bird in the world. Read more about superb starlings in the Natural History article The Secret Lives of Starlings!

Today we release the chromosome-length genome assembly for the superb starling. This genome assembly is an upgrade of CU_Lasu_v1 assembly from the recent paper by Dustin Rubenstein and coauthors (Rubenstein et al. 2021). The paper uses functional genomics to explore the developmental basis of iridescent plumage in superb starlings, which produce both iridescent blue and non-iridescent red feathers.

We thank SeaWorld for their help with the Hi-C sample used for the upgrade!

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.