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Viruses 2017, 9(1), 17; doi:10.3390/v9010017

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

1
Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France
2
Mediterranean Institute of Oceanography (MIO), Aix Marseille Université, Université de Toulon, CNRS/INSU, IRD, UM 110, 13288 Marseille cedex 09, France
*
Author to whom correspondence should be addressed.
Academic Editor: Bernard La Scola
Received: 30 November 2016 / Revised: 13 January 2017 / Accepted: 13 January 2017 / Published: 20 January 2017
(This article belongs to the Special Issue Viruses of Protozoa)
View Full-Text   |   Download PDF [603 KB, uploaded 20 January 2017]   |  

Abstract

The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets—many of which are from algae and aquatic protists—contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity. View Full-Text
Keywords: nucleo-cytoplasmic large DNA virus; lateral gene transfer; virus insertion nucleo-cytoplasmic large DNA virus; lateral gene transfer; virus insertion
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Gallot-Lavallée, L.; Blanc, G. A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses 2017, 9, 17.

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