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Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8609-8614. doi: 10.1073/pnas.1807598115. Epub 2018 Aug 6.

Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion.

Author information

1
Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
2
Berlin Center for Genomics in Biodiversity Research (BeGenDiv), 14195 Berlin, Germany.
3
Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
4
Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus.
5
Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4067, Australia.
6
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
7
Department of Human Genetics, Medical Faculty, University of Saarland, 66421 Homburg, Germany.
8
Max Delbruck Center, The Berlin Institute for Medical Systems Biology, Genomics, 13125 Berlin, Germany.
9
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055.
10
Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia.
11
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; roca@illinois.edu greenwood@izw-berlin.de.
12
Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; roca@illinois.edu greenwood@izw-berlin.de.
13
Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany.

Abstract

Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.

KEYWORDS:

endogenous retrovirus; genome evolution; koala retrovirus; recombination; retrovirus

PMID:
30082403
PMCID:
PMC6112702
DOI:
10.1073/pnas.1807598115
[Indexed for MEDLINE]
Free PMC Article

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