Journal article
Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline
Scientific Reports, Vol.7, 15838
2017
Abstract
The koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus). KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an individual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites. Most integrations contain full-length, endogenous provirus; KoRV-A subtype. The second most frequent integrations contain an endogenous recombinant element (recKoRV) in which most of the KoRV protein-coding region has been replaced with an ancient, endogenous retroelement. A third set of integrations, with very low sequence coverage, may represent somatic cell integrations of KoRV-A, KoRV-B and two recently designated additional subgroups, KoRV-D and KoRV-E. KoRV-D and KoRV-E are missing several genes required for viral processing, suggesting they have been transmitted as defective viruses. Our results represent the first comprehensive analyses of KoRV integration and variation in a single animal and provide further insights into the process of retroviral-host species interactions.
Details
- Title
- Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline
- Authors
- Matthew Hobbs (Author) - Australian MuseumAndrew King (Author) - Australian MuseumRyan Salinas (Author) - University of New South WalesZhiliang Chen (Author) - University of New South WalesKyriakos Tsangaras (Author) - Leibniz Institute for Zoo and Wildlife Research, GermanyAlex D Greenwood (Author) - Leibniz Institute for Zoo and Wildlife Research, GermanyRebecca N Johnson (Author) - Australian MuseumKatherine Belov (Author) - University of SydneyMarc R Wilkins (Author) - University of New South WalesPeter Timms (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
- Publication details
- Scientific Reports, Vol.7, 15838; 9
- Publisher
- Nature Publishing Group
- Date published
- 2017
- DOI
- 10.1038/s41598-017-16171-1
- ISSN
- 2045-2322
- Copyright note
- Copyright © The Author(s) 2017. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Organisation Unit
- University of the Sunshine Coast, Queensland; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99451190402621
- Output Type
- Journal article
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- Virology
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