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Mobile DNA

, 6:16

First Online: 16 September 2015Received: 03 August 2015Accepted: 10 September 2015


BackgroundThe discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host endogenous viral elements; EVEs has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod Armadillidium nasatum, two water fleas Daphnia pulex and D. pulicaria, two copepods the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis, and a freshwater amphipod Hyalella azteca.

ResultsIn total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae −ssRNA, Circoviridae ssDNA, Mononegavirales −ssRNA, Parvoviridae ssDNA and Totiviridae dsRNA. The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation from none to >10 nonsense mutations suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses.

ConclusionsIn conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species.

KeywordsPaleovirology Endogenous viral elements Virus Bunyaviridae Circoviridae Mononegavirales Parvoviridae Totiviridae Copepoda Crustacea AbbreviationsRdRpRNA-dependent RNA polymerase

PCRPolymerase chain reaction

EVEEndogenous viral element

Electronic supplementary materialThe online version of this article doi:10.1186-s13100-015-0047-3 contains supplementary material, which is available to authorized users.

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Autor: Gabriel Metegnier - Thomas Becking - Mohamed Amine Chebbi - Isabelle Giraud - Bouziane Moumen - Sarah Schaack - Richard Co


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