Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.

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 use...

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Auteurs principaux:	Mickaël Boyer, Mohammed-Amine Madoui, Gregory Gimenez, Bernard La Scola, Didier Raoult
Format:	article
Langue:	EN
Publié:	Public Library of Science (PLoS) 2010
Sujets:	Medicine R Science Q
Accès en ligne:	https://doaj.org/article/e4494fd492e1441aa84e81a2d98d122d
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spelling	oai:doaj.org-article:e4494fd492e1441aa84e81a2d98d122d2021-11-18T07:02:10ZPhylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.1932-620310.1371/journal.pone.0015530https://doaj.org/article/e4494fd492e1441aa84e81a2d98d122d2010-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21151962/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Mickaël BoyerMohammed-Amine MadouiGregory GimenezBernard La ScolaDidier RaoultPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 12, p e15530 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mickaël Boyer Mohammed-Amine Madoui Gregory Gimenez Bernard La Scola Didier Raoult Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
description	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.
format	article
author	Mickaël Boyer Mohammed-Amine Madoui Gregory Gimenez Bernard La Scola Didier Raoult
author_facet	Mickaël Boyer Mohammed-Amine Madoui Gregory Gimenez Bernard La Scola Didier Raoult
author_sort	Mickaël Boyer
title	Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
title_short	Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
title_full	Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
title_fullStr	Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
title_full_unstemmed	Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
title_sort	phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/e4494fd492e1441aa84e81a2d98d122d
work_keys_str_mv	AT mickaelboyer phylogeneticandphyleticstudiesofinformationalgenesingenomeshighlightexistenceofa4domainoflifeincludinggiantviruses AT mohammedaminemadoui phylogeneticandphyleticstudiesofinformationalgenesingenomeshighlightexistenceofa4domainoflifeincludinggiantviruses AT gregorygimenez phylogeneticandphyleticstudiesofinformationalgenesingenomeshighlightexistenceofa4domainoflifeincludinggiantviruses AT bernardlascola phylogeneticandphyleticstudiesofinformationalgenesingenomeshighlightexistenceofa4domainoflifeincludinggiantviruses AT didierraoult phylogeneticandphyleticstudiesofinformationalgenesingenomeshighlightexistenceofa4domainoflifeincludinggiantviruses
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Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.

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