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 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