title: Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family.
abstract: BACKGROUND
  The family Mimiviridae belongs to the large monophyletic group of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV; proposed order Megavirales) and encompasses giant viruses infecting amoeba and probably other unicellular eukaryotes. The recent discovery of the Cafeteria roenbergensis virus (CroV), a distant relative of the prototype mimiviruses, led to a substantial expansion of the genetic variance within the family Mimiviridae. In the light of these findings, a reassessment of the relationships between the mimiviruses and other NCLDV and reconstruction of the evolution of giant virus genomes emerge as interesting and timely goals.
  
  
  RESULTS
  Database searches for the protein sequences encoded in the genomes of several viruses originally classified as members of the family Phycodnaviridae, in particular Organic Lake phycodnaviruses and Phaeocystis globosa viruses (OLPG), revealed a greater number of highly similar homologs in members of the Mimiviridae than in phycodnaviruses. We constructed a collection of 898 Clusters of Orthologous Genes for the putative expanded family Mimiviridae (MimiCOGs) and used these clusters for a comprehensive phylogenetic analysis of the genes that are conserved in most of the NCLDV. The topologies of the phylogenetic trees for these conserved viral genes strongly support the monophyly of the OLPG and the mimiviruses. The same tree topology was obtained by analysis of the phyletic patterns of conserved viral genes. We further employed the mimiCOGs to obtain a maximum likelihood reconstruction of the history of genes losses and gains among the giant viruses. The results reveal massive gene gain in the mimivirus branch and modest gene gain in the OLPG branch.
  
  
  CONCLUSIONS
  These phylogenomic results reported here suggest a substantial expansion of the family Mimiviridae. The proposed expanded family encompasses a greater diversity of viruses including a group of viruses with much smaller genomes than those of the original members of the Mimiviridae. If the OLPG group is included in an expanded family Mimiviridae, it becomes the only family of giant viruses currently shown to host virophages. The mimiCOGs are expected to become a key resource for phylogenomics of giant viruses.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Natalya
authors.initials: N
authors.lastname: Yutin
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D019143:Evolution, Molecular; D005814:Genes, Viral; D016679:Genome, Viral; D056686:Mimiviridae / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D017385:Sequence Homology
references.citation: Virology. 2005 Oct 10;341(1):80-90
references.pmid: 16081120
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31
references.pmid: 15215404
references.citation: Curr Top Microbiol Immunol. 2009;328:89-121
references.pmid: 19216436
references.citation: Syst Biol. 2002 Jun;51(3):492-508
references.pmid: 12079646
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21848-53
references.pmid: 20007369
references.citation: Intervirology. 2010;53(5):321-9
references.pmid: 20551684
references.citation: J Virol. 2001 Dec;75(23):11720-34
references.pmid: 11689653
references.citation: Bioinformatics. 2010 Jun 15;26(12):1481-7
references.pmid: 20439257
references.citation: Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17486-91
references.pmid: 21987820
references.citation: Genome Biol Evol. 2012;4(12):1324-30
references.pmid: 23221609
references.citation: Brief Bioinform. 2011 Sep;12(5):379-91
references.pmid: 21690100
references.citation: Virus Res. 2006 Apr;117(1):156-84
references.pmid: 16494962
references.citation: PLoS One. 2011;6(6):e21080
references.pmid: 21698163
references.citation: Trends Plant Sci. 2012 Jan;17(1):1-8
references.pmid: 22100667
references.citation: Cell Microbiol. 2013 Jan;15(1):24-34
references.pmid: 22978691
references.citation: BMC Evol Biol. 2004 Jun 28;4:18
references.pmid: 15222900
references.citation: Intervirology. 2012;55(5):321-32
references.pmid: 22508375
references.citation: BMC Evol Biol. 2001 Oct 20;1:8
references.pmid: 11734060
references.citation: Adv Virus Res. 2012;82:63-89
references.pmid: 22420851
references.citation: Methods Enzymol. 1996;266:418-27
references.pmid: 8743697
references.citation: Science. 2004 Nov 19;306(5700):1344-50
references.pmid: 15486256
references.citation: Biol Direct. 2012 Oct 04;7:34
references.pmid: 23036091
references.citation: Trends Genet. 2010 Oct;26(10):431-7
references.pmid: 20696492
references.citation: Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19508-13
references.pmid: 20974979
references.citation: Clin Microbiol Rev. 2004 Apr;17(2):413-33
references.pmid: 15084508
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: Curr Opin Virol. 2011 Nov;1(5):381-7
references.pmid: 22440839
references.citation: Intervirology. 2010;53(5):284-92
references.pmid: 20551680
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18078-83
references.pmid: 23071316
references.citation: Science. 2011 Apr 8;332(6026):231-4
references.pmid: 21385722
references.citation: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6163-8
references.pmid: 21444812
references.citation: Genome Biol Evol. 2011;3:737-42
references.pmid: 21705471
references.citation: J Virol. 2013 Apr;87(8):4225-36
references.pmid: 23408616
references.citation: Bioinformatics. 2011 Apr 15;27(8):1164-5
references.pmid: 21335321
references.citation: Virus Res. 2006 Apr;117(1):145-55
references.pmid: 16181700
references.citation: Virus Res. 2006 Apr;117(1):133-44
references.pmid: 16469402
references.citation: BMC Evol Biol. 2012 Aug 24;12:156
references.pmid: 22920653
references.citation: PLoS One. 2011 Apr 29;6(4):e18935
references.pmid: 21559486
references.citation: Nature. 2008 Sep 4;455(7209):100-4
references.pmid: 18690211
references.citation: Genome Biol. 2008;9(7):R106
references.pmid: 18598358
references.citation: Intervirology. 2010;53(5):344-53
references.pmid: 20551686
references.citation: Virol J. 2008 Jan 23;5:12
references.pmid: 18215256
references.citation: Commun Integr Biol. 2012 Jan 1;5(1):102-6
references.pmid: 22482024
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: PLoS One. 2010 Mar 10;5(3):e9490
references.pmid: 20224823
references.citation: Bioinformatics. 2010 Aug 1;26(15):1910-2
references.pmid: 20551134
references.citation: Virol J. 2012 Aug 14;9:161
references.pmid: 22891861
references.citation: Nat Rev Microbiol. 2008 Apr;6(4):315-9
references.pmid: 18311164
references.citation: Viruses. 2011 Jan;3(1):32-46
references.pmid: 21994725
references.citation: Intervirology. 2010;53(5):330-43
references.pmid: 20551685
references.citation: Mol Biol Evol. 2008 Aug;25(8):1619-30
references.pmid: 18463089
references.citation: Virol J. 2009 Dec 17;6:223
references.pmid: 20017929
references.citation: Annu Rev Genet. 2003;37:153-95
references.pmid: 14616059
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147