%0 Journal Article
%T DNA-Dependent RNA Polymerase Detects Hidden Giant Viruses in Published Databanks
%+ Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE)
%+ Institut de Mathématiques de Marseille (I2M)
%+ Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
%+ Assistance Publique - Hôpitaux de Marseille (APHM)
%+ Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U912 INSERM - Aix Marseille Univ - IRD)
%A Sharma, Vikas
%A Colson, Philippe
%A Giorgi, Roch
%A Pontarotti, Pierre
%A Raoult, Didier
%Z Vikas Sharma received a grant from the "Infectiopole Sud" foundation.
%< avec comité de lecture
%@ 1759-6653
%J Genome Biology and Evolution
%I Society for Molecular Biology and Evolution
%V 6
%N 7
%8 2014-06-13
%D 2014
%R 10.1093/gbe/evu128
%K DNA-dependent RNA polymerase
%K giant virus
%K “megavirales”
%K dark matter
%K metagenomes
%K domains of life
%K environment
%Z Life Sciences [q-bio]/Microbiology and Parasitology/Virology
%Z Mathematics [math]Journal articles
%X 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.
%G English
%L hal-01308942
%U https://hal.science/hal-01308942
%~ CNRS
%~ UNIV-AMU
%~ EC-MARSEILLE
%~ I2M
%~ I2M-2014-
%~ U1252