Phylogenetic and Phyletic Studies of Informational Genes in Genomes Highlight Existence of a 4th Domain of Life Including Giant Viruses

被引:109
作者
Boyer, Mickael [1 ]
Madoui, Mohammed-Amine [1 ]
Gimenez, Gregory [1 ]
La Scola, Bernard [1 ]
Raoult, Didier [1 ]
机构
[1] Univ Mediterrane, URMITE, Ctr Natl Rech Sci UMR IRD 6236, Fac Med, Marseille, France
来源
PLOS ONE | 2010年 / 5卷 / 12期
关键词
SEQUENCE; ORIGIN; TREE; REPLICATION; EVOLUTION; DIVERGENT; DATABASE; COMMON; SIRV1;
D O I
10.1371/journal.pone.0015530
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
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页数:8
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共 41 条
  • [1] 5500 Phages examined in the electron microscope
    Ackermann, H. -W.
    [J]. ARCHIVES OF VIROLOGY, 2007, 152 (02) : 227 - 243
  • [2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Altschul, SF
    Madden, TL
    Schaffer, AA
    Zhang, JH
    Zhang, Z
    Miller, W
    Lipman, DJ
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
  • [3] Common ancestry of herpesviruses and tailed DNA bacteriophages
    Baker, ML
    Jiang, W
    Rixon, FJ
    Chiu, W
    [J]. JOURNAL OF VIROLOGY, 2005, 79 (23) : 14967 - 14970
  • [4] Bell PJL, 2001, J MOL EVOL, V53, P251
  • [5] The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses
    Blum, H
    Zillig, W
    Mallok, S
    Domdey, H
    Prangishvili, D
    [J]. VIROLOGY, 2001, 281 (01) : 6 - 9
  • [6] THE ORIGIN OF EUKARYOTE AND ARCHAEBACTERIAL CELLS
    CAVALIERSMITH, T
    [J]. ANNALS OF THE NEW YORK ACADEMY OF SCIENCES, 1987, 503 : 17 - 54
  • [7] The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit
    Dias, Alexandre
    Bouvier, Denis
    Crepin, Thibaut
    McCarthy, Andrew A.
    Hart, Darren J.
    Baudin, Florence
    Cusack, Stephen
    Ruigrok, Rob W. H.
    [J]. NATURE, 2009, 458 (7240) : 914 - 918
  • [8] MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Edgar, RC
    [J]. NUCLEIC ACIDS RESEARCH, 2004, 32 (05) : 1792 - 1797
  • [9] Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses
    Filee, Jonathan
    Pouget, Noelle
    Chandler, Mick
    [J]. BMC EVOLUTIONARY BIOLOGY, 2008, 8 (1)