Genome Biology (Jan 2023)
The swan genome and transcriptome, it is not all black and white
- Anjana C. Karawita,
- Yuanyuan Cheng,
- Keng Yih Chew,
- Arjun Challagulla,
- Robert Kraus,
- Ralf C. Mueller,
- Marcus Z. W. Tong,
- Katina D. Hulme,
- Helle Bielefeldt-Ohmann,
- Lauren E. Steele,
- Melanie Wu,
- Julian Sng,
- Ellesandra Noye,
- Timothy J. Bruxner,
- Gough G. Au,
- Suzanne Lowther,
- Julie Blommaert,
- Alexander Suh,
- Alexander J. McCauley,
- Parwinder Kaur,
- Olga Dudchenko,
- Erez Aiden,
- Olivier Fedrigo,
- Giulio Formenti,
- Jacquelyn Mountcastle,
- William Chow,
- Fergal J. Martin,
- Denye N. Ogeh,
- Françoise Thiaud-Nissen,
- Kerstin Howe,
- Alan Tracey,
- Jacqueline Smith,
- Richard I. Kuo,
- Marilyn B. Renfree,
- Takashi Kimura,
- Yoshihiro Sakoda,
- Mathew McDougall,
- Hamish G. Spencer,
- Michael Pyne,
- Conny Tolf,
- Jonas Waldenström,
- Erich D. Jarvis,
- Michelle L. Baker,
- David W. Burt,
- Kirsty R. Short
Affiliations
- Anjana C. Karawita
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney
- Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Arjun Challagulla
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness
- Robert Kraus
- Department of Migration, Max Planck Institute of Animal Behavior
- Ralf C. Mueller
- Department of Migration, Max Planck Institute of Animal Behavior
- Marcus Z. W. Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Katina D. Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Lauren E. Steele
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Melanie Wu
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Julian Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Ellesandra Noye
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Timothy J. Bruxner
- Institute for Molecular Bioscience, The University of Queensland
- Gough G. Au
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness
- Suzanne Lowther
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness
- Julie Blommaert
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory
- Alexander Suh
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory
- Alexander J. McCauley
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness
- Parwinder Kaur
- School of Agriculture and Environment, The University of Western Australia
- Olga Dudchenko
- The Centre for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine
- Erez Aiden
- School of Agriculture and Environment, The University of Western Australia
- Olivier Fedrigo
- The Vertebrate Genome Laboratory, The Rockefeller University
- Giulio Formenti
- The Vertebrate Genome Laboratory, The Rockefeller University
- Jacquelyn Mountcastle
- The Vertebrate Genome Laboratory, The Rockefeller University
- William Chow
- Tree of Life, Welcome Sanger Institute
- Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Denye N. Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Françoise Thiaud-Nissen
- National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Kerstin Howe
- Tree of Life, Welcome Sanger Institute
- Alan Tracey
- Tree of Life, Welcome Sanger Institute
- Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus
- Richard I. Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus
- Marilyn B. Renfree
- School of Biosciences, The University of Melbourne
- Takashi Kimura
- Faculty of Veterinary Medicine, Hokkaido University
- Yoshihiro Sakoda
- Faculty of Veterinary Medicine, Hokkaido University
- Mathew McDougall
- New Zealand Fish & Game – Eastern Region
- Hamish G. Spencer
- Department of Zoology, University of Otago
- Michael Pyne
- Currumbin Wildlife Sanctuary
- Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University
- Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University
- Erich D. Jarvis
- The Vertebrate Genome Laboratory, The Rockefeller University
- Michelle L. Baker
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness
- David W. Burt
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland
- DOI
- https://doi.org/10.1186/s13059-022-02838-0
- Journal volume & issue
-
Vol. 24,
no. 1
pp. 1 – 24
Abstract
Abstract 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.
Keywords
