title: A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window.
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.
authors.affiliation: Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France. lucie.gallot-lavallee@igs.cnrs-mrs.fr.
authors.forename: Lucie
authors.initials: L
authors.lastname: Gallot-Lavallée
authors.affiliation: Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France. guillaume.blanc@igs.cnrs-mrs.fr.|Mediterranean Institute of Oceanography (MIO), Aix Marseille Université, Université de Toulon, CNRS/INSU, IRD, UM 110, 13288 Marseille cedex 09, France. guillaume.blanc@igs.cnrs-mrs.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Blanc
mesh_terms: D044822:Biodiversity; D056890:Eukaryota / Q000235:genetics* / Q000821:virology*; D023281:Genomics; D000072139:Giant Viruses / Q000145:classification* / Q000235:genetics*; D011995:Recombination, Genetic
keywords: lateral gene transfer; nucleo-cytoplasmic large DNA virus; virus insertion