A-maize-ing snake

Meet the corn snake Pantherophis guttatus! This snake unfortunately resembles the venomous copperhead and is often killed as a result of this mistaken identity. The truth is that corn snakes lack functional venom and are harmless to humans (although they will strike if disturbed).

Photo Description: A corn snake couple (Pantherophis guttatus). Photo credits: Tanya Orsini [Public domain], via flickr.com

The corn snake is found throughout the southeastern and central United States and is named for the species' regular presence near grain stores, where it preys on mice and rats that eat harvested corn. The Oxford English Dictionary cites this usage as far back as 1675, whilst other sources maintain that the corn snake is so-named because the distinctive, nearly-checkered pattern of the snake's belly scales resembles the kernels of variegated corn.

American corn snakes are popular pets everywhere except Australia. It is a prohibited invasive animal in Australia under the Biosecurity Act of 2014. If released into the wild in Australia, corn snakes could prey on and out-compete native species.

Today we share a chromosome-length assembly for Pantherophis guttatus based on the draft generated by Ullate-Agote et al 2014 & Ullate-Agote et al 2020. We are grateful to Shedd Aquarium for their help with the Hi-C sample used for the upgrade! We are also grateful to the DNA Zoo Australia team at the University of Western Australia and Pawsey Supercomputing Centre for the computational support for this genome assembly. We hope that the new chromosome-length genome assembly will help promote corn snakes as a model species.

Check out the interactive Juicebox.js instance below for the interactive Hi-C contact map of the 18 corn snake chromosomes, and visit the assembly page for more detail!

Born to roan

The roan antelope, Hippotragus equinus, is a member of the horse-like antelope tribe Hippotragini (híppos means horse in Greek). One of the largest antelope species, the roan antelope may weigh as much as 300 kg and can be as tall as 160 cm in height at the shoulders, similar to the height of an average horse [1]. Their vernacular name comes from their reddish-brown (roan) coats but roan antelopes also have a striking white and black facial markings that set them apart from other species. The size of the roan antelope, their curved horns along with an aggressive temperament when threatened make them quite formidable opponents to their predators [2].

Roan Antelope (Hippotragus equinus) by Nik Barrow, [CC BY-NC 2.0], via flickr.com

Today, we release the chromosome-length assembly for the roan antelope, Hippotragus equinus. This assembly is a Hi-C upgrade for the draft genome assembly generated by Gonçalves et al., (2021). Please visit our Methods page for more details on the assembly procedure, and check out the interactive Juicebox.js map below for the Hi-C contact map of the 30 chromosomes of the roan antelope!

Interested in more antelope species? Check out the assembly pages for the sable antelope (Hippotragus niger), Scimitar-horned oryx (Oryx dammah), and the Eastern bongo (Tragelaphus eurycerus isaaci). Subscribe to our mailing list below or follow us on Twitter (@thednazoo) to keep up to date with our newest releases coming in 2022!

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.