title: The genome of the nucleopolyhedrosis-causing virus from Tipula oleracea sheds new light on the Nudiviridae family.
abstract: A large double-stranded DNA (dsDNA) virus that produces occlusion bodies, typical of baculoviruses, has been described to infect crane fly larvae of the genus Tipula (Diptera, Tipulidae). Because of a lack of genomic data, this virus has remained unclassified. Electron microscopy of an archival virus isolated from Tipula oleracea, T. oleracea nudivirus (ToNV), showed irregularly shaped occlusion bodies measuring from 2 to 5 μm in length and 2 μm in middiameter, filled with rod-shape virions containing single nucleocapsids within a bilayer envelope. Whole-genome amplification and Roche 454 sequencing revealed a complete circular genome sequence of 145.7 kb, containing five direct repeat regions. We predicted 131 open reading frames, including a homolog of the polyhedrin gene encoding the major occlusion body protein of T. paludosa nucleopolyhedrovirus (NPV). BLAST searches demonstrated that ToNV had 21 of the 37 baculovirus core genes but shared 52 genes with nudiviruses (NVs). Phylogenomic analyses indicated that ToNV clearly belongs to the Nudiviridae family but should probably be assigned to a new genus. Among nudiviruses, ToNV was most closely related to the Penaeus monodon NV and Heliothis zea NV clade but distantly related to Drosophila innubia NV, the other nudivirus infecting a Diptera. Lastly, ToNV was found to be most closely related to the nuvidirus ancestor of bracoviruses. This was also reflected in terms of gene content, as ToNV was the only known exogenous virus harboring homologs of the Cc50C22.6 and 27b (Cc50C22.7) genes found in the nudiviral genomic cluster involved in bracovirus particle production.
  
  
  OBJECTIVE
  The Nudiviridae is a family of arthropod dsDNA viruses from which striking cases of endogenization have been reported (i.e., symbiotic bracoviruses deriving from a nudivirus and the endogenous nudivirus of the brown planthopper). Although related to baculoviruses, relatively little is known about the genomic diversity of exogenous nudiviruses. Here, we characterized, morphologically and genetically, an archival sample of the Tipula oleracea nudivirus (ToNV), which has the particularity of forming occlusion bodies. Comparative genomic and phylogenomic analyses showed ToNV to be to date the closest known relative of the exogenous ancestor of bracoviruses and that ToNV should be assigned to a new genus. Moreover, we revised the homology relationships of nudiviral genes and identified a new set of 32 core genes for the Nudiviridae, of which 21 were also baculovirus core genes. These findings provide important insights into the evolutionary history of large arthropod dsDNA viruses.
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte (IRBI), CNRS UMR 7261, Université François Rabelais, Tours, France annie.bezier@univ-tours.fr.
authors.forename: Annie
authors.initials: A
authors.lastname: Bézier
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte (IRBI), CNRS UMR 7261, Université François Rabelais, Tours, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Thézé
authors.affiliation: Commissariat à l'Energie Atomique, Génoscope (Centre National de Séquençage, CEA), Evry, France.
authors.forename: Frederick
authors.initials: F
authors.lastname: Gavory
authors.affiliation: Laboratoire de Biologie Cellulaire, Microscopie Electronique, Faculté de Médecine, Université François Rabelais, Tours, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Gaillard
authors.affiliation: Commissariat à l'Energie Atomique, Génoscope (Centre National de Séquençage, CEA), Evry, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte (IRBI), CNRS UMR 7261, Université François Rabelais, Tours, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Drezen
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte (IRBI), CNRS UMR 7261, Université François Rabelais, Tours, France.
authors.forename: Elisabeth A
authors.initials: EA
authors.lastname: Herniou
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D004267:DNA Viruses / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004175:Diptera / Q000821:virology*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D017924:Nucleopolyhedroviruses / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016366:Open Reading Frames; D010802:Phylogeny; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins