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.
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.