Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.
Highlights
The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions
In order to address this question, and to shed new light on the dynamics of viral endogenization more generally, we extended our screen to another species of terrestrial isopod (A. nasatum) and to five additional crustacean species
Endogenous viral element (EVE) abundance and diversity in crustacean genomes Overall, our comprehensive screening for EVEs in six crustacean genomes led to the discovery of a total of 210 EVEs belonging to five viral groups (Bunya, Circo, Parvo, Toti-viridae and Mononegavirales; Figs. 1 and 2)
Summary
The 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. We uncovered 54 EVEs from 10 diverse lineages belonging to the Bunyaviridae, Circoviridae, Parvoviridae and Totiviridae families as well as to the Mononegavirales order, indicating that isopods have been and may still be exposed to a remarkable diversity of viruses These findings extended the host range of all five viral groups to isopod crustaceans, and led to the question of whether A. vulgare is unique in terms of abundance and diversity of EVEs among crustaceans or if a diverse EVE biota is characteristic of the group as a whole. In order to address this question, and to shed new light on the dynamics of viral endogenization more generally, we extended our screen to another species of terrestrial isopod (A. nasatum) and to five additional crustacean species (two species of water flea [Daphnia pulex and Daphnia pulicaria], a marine copepod [Eurytemora affinis], a freshwater amphipod [Hyalella azteca], and the salmon louse [Lepeophtheirus salmonis; Copepoda]; Additional file 1: Figure S1)
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