Pig deal of a turtle

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!

Photo Description: The Pig-nosed turtle (Carettochelys insculpta) Photo credits: Photograph by Wilth licensed under CC BY-NC-SA 2.0 [Source link: https://search.creativecommons.org/photos/22e0f3d2-8a1d-4ca6-bf49-c9cd69553cca]

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.

Emblem of Western Australia - the black swan

The black swan (Cygnus atratus) is a large waterbird, a species of swan, native to Western Australia. The black swan's role in Australian heraldry and culture extends to the first founding of the colonies in the eighteenth century. It has often been equated with antipodean identity, the contrast to the white swan of the northern hemisphere indicating 'Australianness'. The black swan is featured on the flag, and is both the state bird and state emblem of Western Australia; it also appears in the Coat of Arms and other iconography of the state's institutions including our University of Western Australia.

The Australian black swan (Cygnus atratus) Photo Credits & acknowledgements – Parwinder Kaur, [CC BY 2.0]

The Noongar People of the South-West of Australia call the black swan Kooldjak along the West and South-West coast, Gooldjak in the South East and it is sometimes referred to as maali in language schools. The black swan is widely referenced in Australian culture, although the character of that importance historically diverges between the prosaic in the East and the symbolic in the West. The black swan is also of spiritual significance in the traditional histories of many Australian Aboriginal peoples across southern Australia.

Within Australia, the black swan is nomadic, with erratic migration patterns dependent upon climatic conditions. It is a large bird with mostly black plumage and a red bill. The black swan was introduced to various countries as an ornamental bird in the 1800s, but has managed to form stable populations. Black swans can be found singly, or in loose companies numbering into the hundreds or even thousands. It is a popular bird in zoological gardens and bird collections, and escapees are sometimes seen outside their natural range. The black swan is fully protected in all states and territories of Australia and must not be shot.

The black swan is almost exclusively herbivorous, and while there is some regional and seasonal variation, the diet is generally dominated by aquatic and marshland plants. Like other swans, the black swan is largely monogamous, pairing for life with about 6% divorce rate [1].

DNA Zoo has been working in collaboration with Prof Dave Burt, Dr Kirsty Short and Anjana Karawita at the University of Queensland, Australia to map the genome of the black swan at chromosome-length in an effort to understand immune responses to the deadly ‘bird flu’ virus and better protect public health. Here, we use in situ Hi-C to complete a chromosome-length assembly of the black swan.

The chromosome-length assembly we share today is based on the primary assembly by the University of Queensland team, led by Dr Kirsty Short and PhD candidate Anjana Karawita shared on NCBI. This draft assembly was scaffolded with 98,929,251 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

The Hi-C work 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 with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government, the Government of Western Australia and Dr. Short’s ARC DECRA grant (DE180100512).

The genome of a black swan will hopefully help us understand why these birds are extremely susceptible to the bird flu virus [2]. Right now, our UQ based research collaborators (Dr. Kirsty Short’s lab) are working on annotating the immune genes in the black swan genome assembly and comparing them to genes in the closely related mute swan genome and other avian species less susceptible to bird flu to build a better understanding their immune responses to the highly pathogenic avian influenza (HPAI) aka the bird flu.

Given the virus can occasionally spill over into humans with devastating consequences. Since 2003, this virus has only infected approximately 800 people worldwide, however, more than 50% of infected individuals have not survived the disease. It is important we know more about disease with zoonotic potential early - a key lesson from the current pandemic!

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.

Blog by: Parwinder Kaur, Anjana Karawita, Dave Burt and Kirsty Short

Get a sneak peek at the chromosome-length contact map for the black swan below, and don't forget to visit the assembly page https://www.dnazoo.org/assemblies/Cygnus_atratus for more details and statistics!

Citations

Kraaijeveld, Ken; Gregurke, John; Hall, Carol; Komdeur, Jan & Mulder, Raoul A. (May 2004). "Mutual ornamentation, sexual selection, and social dominance in the black swan". Behavioral Ecology. 15 (3): 380–389. doi:10.1093/beheco/arh023

Short KR, Veldhuis Kroeze EJ, Reperant LA, Richard M, Kuiken T. (Dec 2014). Influenza virus and endothelial cells: a species-specific relationship. Front Microbiol. 2014;5:653. doi:10.3389/fmicb.2014.00653

The Model Legume - Medicago truncatula R108

Medicago truncatula aka barrelclover is an annual legume native to the Mediterranean region. It is a low-growing, clover-like plant 10–60 centimetres (3.9–23.6 in) tall with trifoliate leaves. Each leaflet is rounded, 1–2 centimetres (0.39–0.79 in) long, often with a dark spot in the center. The flowers are yellow, produced singly or in a small inflorescence of two to five together; the fruit is a small, spiny pod.

Medicago truncatula flower1 Denman, photo by Harry Rose [CC BY 2.0], via flickr.com.

This species is studied as a model organism for legumes, a plant family that includes soybeans, peanuts, peas and alfalfa, because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production. As such, extensive genomic studies of the species have been undertaken, and a genome assembly for the species has been available to the community thanks to the efforts of the Medicago truncatula Consortium (see Young et al., 2017; Tang et al., 2014).

Unfortunately, the reference genotype (Jemalong A17) originally selected for the chromosome-length genome sequencing and assembly proved to be recalcitrant to transformation. M. truncatula R108 accession is more attractive for genetic studies due to its high transformation efficiency and functional genomic resources, but has been lacking a chromosome-length genome assembly.

To address this we performed in situ Hi-C (~30×) to anchor, order, orient scaffolds, and correct misjoins in contigs from a draft genome assembly for the R108 barrelclover from (Moll et al., 2017) resulting in a chromosome-length genome assembly. The new assembly allowed us to accurately annotate the chromosome 4/8 translocation between the R105 and A17 accessions as well as map the Tnt1 retrotransposon insertions creating a resource for downstream insertional mutagenesis studies. Read more about this in our research article “Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly” now available open access in IJMS, Special Issue - Functional Genomics for Plant Breeding 2.0.

We gratefully acknowledge the frozen leaf sample provided by Scott Schaeffer at the Nakata Lab (USDA, ARS). The Hi-C work was enabled 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.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Christopher Lui, Melanie Pham, Olga Dudchenko, Erez Aiden & Parwinder Kaur.

Blog by: Parwinder Kaur