The swan genome and transcriptome, its not all black and white

Anjana C. Karawita, Yuanyuan Cheng, Keng Yih Chew, Arjun Challgula, Robert Kraus, Ralf C. Mueller, Marcus Z. W. Tong, Katina D. Hulme, Helle Beielefeldt-Ohmann, Lauren Steel, Melanie Wu, Julian Sng, Ellesandra Noye, Timothy G. Bruxner, Gough G. Au, Suzanne Lowther, Julie Blommaert, Alexander Suh, Alexander McCauley, Parwinder KaurOlga Dudchenko , Erez Aiden, Olivier Fedrigo, Giulio Formenti, Jacquelyn Mountcastle, William Chow, Erich D Jarvis, Fergal J Martin, Denye N. Ogeh, Françoise Thiaud-Nissen, Kerstin Howe, Joanna Collins, Alan Tracey, Jacqueline Smith, Richard Kuo, Marilyn B Renfree, Takashi Kimura, Yoshihiro Sakoda, Mathew McDougall, Hamish G. Spencer, Michael Pyne, Conny Tolf, Jonas Waldenström, Michelle L. Barker, David Burt, Kirsty R. Short

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

BACKGROUND: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.

RESULTS: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.

CONCLUSION: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Original languageEnglish
Article number13
JournalGenome Biology
Issue number1
Early online date23 Jan 2023
Publication statusPublished - 23 Jan 2023

Keywords / Materials (for Non-textual outputs)

  • Animals
  • Anseriformes
  • Australia
  • Endothelial Cells
  • Influenza in Birds
  • Transcriptome


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