title: DNA-dependent RNA polymerase detects hidden giant viruses in published databanks.
abstract: Environmental metagenomic studies show that there is a "dark matter," composed of sequences not linked to any known organism, as determined mainly using ribosomal DNA (rDNA) sequences, which therefore ignore giant viruses. DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes. We found while reconstructing RNAP subunit 2 (RNAP2) phylogeny that a giant virus sequenced together with the genome of a large eukaryote, Hydra magnipapillata, has been overlooked. To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and an oomycete plant pathogen, and detected unknown putative viral clades. We suggest using RNAP systematically to decipher the black matter and identify giant viruses.
authors.affiliation: Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, FranceAix-Marseille Univ., I2M UMR-CNRS 7373, Evolution Biologique et Modélisation, Marseille, France.
authors.forename: Vikas
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, FranceFondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
authors.affiliation: Aix-Marseille Université, UMR S 912 (SESSTIM), INSERM, IRD, Marseille, FranceAssistance Publique-Hôpitaux de Marseille, hôpital Timone, Service Biostatistique et Technologies de l'Information et de la Communication, Marseille, France.
authors.forename: Roch
authors.initials: R
authors.lastname: Giorgi
authors.affiliation: Aix-Marseille Univ., I2M UMR-CNRS 7373, Evolution Biologique et Modélisation, Marseille, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.affiliation: Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, FranceFondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France didier.raoult@gmail.com.
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000818:Animals; D004247:DNA / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D030541:Databases, Genetic; D016679:Genome, Viral; D006829:Hydra / Q000235:genetics / Q000821:virology; D010802:Phylogeny
chemical_list: D004247:DNA; D012321:DNA-Directed RNA Polymerases
keywords: DNA-dependent RNA polymerase; Mimivirus; dark matter; domains of life; environment; giant virus; metagenomes; “Megavirales”