The swan genome and transcriptome, it is not all black and white

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander ORCID:, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W. and Short, Kirsty R. (2023) The swan genome and transcriptome, it is not all black and white. Genome Biology, 24. ISSN 1474-760X

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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.

Item Type: Article
Additional Information: Funding information: This study was funded by the Australian Department of Agriculture and Water Resources (CSIRO Science and Innovation Award; KRS), the Australian Department of Agriculture and Water Resources (Australian Eggs Innovation Award; KRS), and an Australian Research Council DECRA (DE180100512; KRS). This research was funded in part by the Wellcome Trust [Grant numbers 108749/Z/15/Z, 222155/Z/20/Z]. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. ACK was supported by the Australian Government’s research training program (RTP) scholarship. PK is supported by the University of Western Australia with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and Government of Western Australia. Hi-C data for the Black Swan was created by the DNA Zoo Consortium ( DNA Zoo sequencing effort is supported by Illumina, Inc. E.L.A. was supported by the Welch Foundation (Q-1866- 20210327), an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375), a US-Israel Binational Science Foundation Award (2019276), the Behavioral Plasticity Research Institute (NSF DBI-2021795), NSF Physics Frontiers Center Award (NSF PHY-2019745), and an NIH CEGS (RM1HG011016-01A1).
Uncontrolled Keywords: black swan,genomes,virology,genetics,ecology, evolution, behavior and systematics,cell biology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1311
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 20 Feb 2023 12:30
Last Modified: 06 Apr 2024 11:31
DOI: 10.1186/s13059-022-02838-0


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