title: Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
abstract: The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya, with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria and Archaea. We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life.
authors.affiliation: URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
authors.forename: Mickaël
authors.initials: M
authors.lastname: Boyer
authors.forename: Mohammed-Amine
authors.initials: MA
authors.lastname: Madoui
authors.forename: Gregory
authors.initials: G
authors.lastname: Gimenez
authors.forename: Bernard
authors.initials: B
authors.lastname: La Scola
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D016000:Cluster Analysis; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D019766:Genes, Archaeal; D005798:Genes, Bacterial / Q000235:genetics; D016678:Genome; D016679:Genome, Viral; D008957:Models, Genetic; D010802:Phylogeny; D012270:Ribosomes / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014780:Viruses / Q000235:genetics*