The Pig-nosed turtle (Carettochelys insculpta) is the sole surviving member of its entire family, Carettochelyidae, and sits alone on a branch of the tree of life reaching back around 140 million years. That is more than 70 million years before the extinction of the dinosaurs!
This strange turtle has a large leathery shell 60-70 cm with no distinct scutes and has a long, fleshy snout with large nostrils, much like that of a pig (hence the common name of the species). This unique freshwater turtle has many unusual morphological, ecological and behavioural characteristics. Unlike other freshwater turtles, the pig-nosed turtle has broad paddle-like flippers, each with two claws, resembling those of a sea turtle more than a freshwater species [1].
The pig-nosed turtle is a relict both evolutionarily and geographically, with its current distribution likely reflecting a previous era when Australia was connected to New Guinea [2]. In Australia, the pig-nosed turtle is an endemic of only a few rivers within the Northern Territory, while it has a much greater distribution across much of southern New Guinea. The increased commercial activity across its range in New Guinea is bringing the species into closer contact with humans. The species is threatened by increased demand for individuals and eggs, for both food and the international pet trade [3]. Livestock, feral animals and agriculture also threaten the habitat of the species in Australia [4].
Today, we share the chromosome-length upgrade to the publicly available draft Carettochelys_insculpta-1.0 (GCA_007922185.1) generated by Brad Shaffer (University of Los Angeles), Patrick Minx (Washington University School of Medicine) and Peter Scott (West Texas A&M University).
The specimen that was used for the upgrade was collected by Matthew Young in collaboration with the Njanjma Rangers, traditional owners of West Arnhem, and was supported by funding from the Holsworth Wildlife Research Endowment Fund under the supervision of Arthur Georges at the University of Canberra, Australia. This effort has been supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), an initiative of Bioplatforms Australia building genomic resources for thorough understanding of evolution and conservation of Australia’s unique native amphibians and reptiles that are now under threat, through climate, disease or habitat modification.
The Hi-C work for the chromosome-length upgrade 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.
Decoding the genetic blueprint of this endangered species with the addition of chromosome conformation scaffolding will assist in many ways with its conservation and management. Wildlife trafficking for the illegal pet trade and traditional medicines is a concerning threat for the persistence of wild populations of pig-nosed turtles. This will also facilitate developing wildlife forensics resources for the assignment of provenance of trafficked individuals to their source populations, to combat the illegal trade and to aid conservation work repatriating seized pig-nosed turtles.
The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.
Citations
1. Cogger, H.G. 2018. Reptiles and Amphibians of Australia. CSIRO Publishing, Canberra Australia.
2. Cogger, H.G. & Heatwole, H. (1981). The Australian reptiles: Origins, biogeography, distribution patterns and island evolution. Monographia Biologicae 41:1331-1373.
3. Shepherd, C.R., Gomez, L. & Nijman, V. (2020). Illegal wildlife trade, seizures and prosecutions: a 7.5-year analysis of trade in pig-nosed turtles Carettochelys insculpta in and from Indonesia. Global Ecology and Conservation. 24, p.e01249.
4. Eisemberg, C., van Dijk, P.P., Georges, A. & Amepou, Y. (2018). Carettochelys insculpta. The IUCN Red List of Threatened Species 2018: e.T3898A2884984. https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T3898A2884984.en. Downloaded on 08 April 2021.