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Host evolutionary history and ecology shape virome composition in fishes

View ORCID ProfileJemma L. Geoghegan, Francesca Di Giallonardo, Michelle Wille, Ayda Susana Ortiz-Baez, Vincenzo A. Costa, Timothy Ghaly, Jonathon C. O. Mifsud, Olivia M. H. Turnbull, David R. Bellwood, Jane E. Williamson, Edward C. Holmes
doi: https://doi.org/10.1101/2020.05.06.081505
Jemma L. Geoghegan
1Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
3Institute of Environmental Science and Research, Wellington 5018, New Zealand
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  • ORCID record for Jemma L. Geoghegan
  • For correspondence: jemma.geoghegan@otago.ac.nz
Francesca Di Giallonardo
4The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
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Michelle Wille
5WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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Ayda Susana Ortiz-Baez
6Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Vincenzo A. Costa
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Timothy Ghaly
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Jonathon C. O. Mifsud
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Olivia M. H. Turnbull
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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David R. Bellwood
7ARC Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
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Jane E. Williamson
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Edward C. Holmes
6Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Abstract

Identifying the components of host ecology that promote virus diversity is crucial for our understanding of the drivers of virus evolution and disease emergence. As the most species-rich group of vertebrates that exhibit diverse ecologies, fish provide an ideal model system to study the impacts of host ecology on the composition of their viromes. To better understand the factors that shape virome composition in marine fishes, we characterised the viromes of 23 fish species (19 from this study and four that were sampled previously (Geoghegan et al 2018a)) using unbiased bulk RNA-sequencing (meta-transcriptomics) together with both sequence and protein structural homology searches to identify divergent viruses that often evade characterisation. These data revealed that fish virome composition – that is, viral richness, abundance and diversity – were predominantly shaped by the phylogenetic history of their hosts, as reflected in taxonomic order. In addition, preferred mean water temperature, climate, habitat depth, community diversity and whether fish swim in schools or are solitary were identified as important ecological features that shaped virome diversity and abundance in these fish. Our analysis also identified 25 new virus transcripts that could be assigned to 11 different viral families, including the first fish virus in the Matonaviridae. Other viruses identified fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae and Flaviviridae. Our results provide a better understanding of the ecological determinants of virome diversity and support the view that fish harbour a multitude of viruses, of which the vast majority are undescribed.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Host evolutionary history and ecology shape virome composition in fishes
Jemma L. Geoghegan, Francesca Di Giallonardo, Michelle Wille, Ayda Susana Ortiz-Baez, Vincenzo A. Costa, Timothy Ghaly, Jonathon C. O. Mifsud, Olivia M. H. Turnbull, David R. Bellwood, Jane E. Williamson, Edward C. Holmes
bioRxiv 2020.05.06.081505; doi: https://doi.org/10.1101/2020.05.06.081505
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Host evolutionary history and ecology shape virome composition in fishes
Jemma L. Geoghegan, Francesca Di Giallonardo, Michelle Wille, Ayda Susana Ortiz-Baez, Vincenzo A. Costa, Timothy Ghaly, Jonathon C. O. Mifsud, Olivia M. H. Turnbull, David R. Bellwood, Jane E. Williamson, Edward C. Holmes
bioRxiv 2020.05.06.081505; doi: https://doi.org/10.1101/2020.05.06.081505

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