T. Adekambi, M. Drancourt, R. , and D. , The rpoB gene as a tool for clinical microbiologists, Trends Microbiol, vol.17, pp.37-45, 2009.

S. Aherfi, M. Boughalmi, I. Pagnier, G. Fournous, L. Scola et al., Complete genome sequence of tunisvirus, a new member of the proposed family marseilleviridae, Arch. Virol, vol.159, pp.2349-2358, 2014.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.80360-80362, 1990.
DOI : 10.1006/jmbi.1990.9999

M. H. Antwerpen, E. Georgi, L. Zoeller, R. Woelfel, K. Stoecker et al., Whole-genome sequencing of a pandoravirus isolated from keratitis-inducing acanthamoeba, Genome Announc, vol.3, pp.136-00115, 2015.

D. Arslan, M. Legendre, V. Seltzer, C. Abergel, C. et al., Distant mimivirus relative with a larger genome highlights the fundamental features of megaviridae, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.17486-17491, 2011.

M. Boyer, M. A. Madoui, G. Gimenez, L. Scola, B. et al., Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses, PLoS ONE, vol.5, p.15530, 2010.

M. Boyer, N. Yutin, I. Pagnier, L. Barrassi, G. Fournous et al., Giant marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.21848-21853, 2009.

R. J. Case, Y. Boucher, I. Dahllof, C. Holmstrom, W. F. Doolittle et al., Use Of 16s rRNA and rpoB genes as molecular markers for microbial ecology studies, Appl. Environ. Microbiol, vol.73, pp.278-288, 2007.

P. Colson, X. De-lamballerie, N. Yutin, S. Asgari, Y. Bigot et al., Megavirales, " a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses, Arch. Virol, vol.158, pp.2517-2521, 2013.
DOI : 10.1007/s00705-013-1768-6
URL : https://hal.archives-ouvertes.fr/hal-01129809

P. Colson, G. Gimenez, M. Boyer, G. Fournous, R. et al., The giant cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of life, PLoS ONE, vol.6, 2011.

R. C. Edgar, Muscle: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340
URL : http://europepmc.org/articles/pmc390337?pdf=render

J. Filee, Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of The Iceberg? Virology 466-467, 2014.

J. Filee, P. Forterre, T. Sen-lin, L. , and J. , Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins, J. Mol. Evol, vol.54, pp.763-773, 2002.

J. Filee, N. Pouget, C. , and M. , Phylogenetic evidence for extensive lateral acquisition of cellular genes by nucleocytoplasmic large DNA viruses, BMC Evol. Biol, vol.8, p.320, 2008.

M. G. Fischer, M. J. Allen, W. H. Wilson, and C. A. Suttle, Giant virus with a remarkable complement of genes infects marine zooplankton, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.19508-19513, 2010.

S. B. Hedges, J. Dudley, and S. Kumar, Timetree: a public knowledgebase of divergence times among organisms, Bioinformatics, vol.22, pp.2971-2972, 2006.

L. M. Iyer, L. Aravind, and E. V. Koonin, Common origin of four diverse families of large eukaryotic DNA viruses, J. Virol, vol.75, pp.11720-11734, 2001.

L. M. Iyer, S. Balaji, E. V. Koonin, A. , and L. , Evolutionary genomics of nucleo-cytoplasmic large DNA viruses, Virus Res, vol.117, pp.156-184, 2006.

E. V. Koonin, Y. , and N. , Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses, Intervirology, vol.53, pp.284-292, 2010.

L. Scola, B. Audic, S. Robert, C. Jungang, L. De-lamballerie et al., A giant virus in amoebae, Science, vol.299, p.2033, 2003.

M. Legendre, J. Bartoli, L. Shmakova, S. Jeudy, K. Labadie et al., Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.4274-4279, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02193478

L. Li, C. J. Stoeckert, R. , and D. S. , Orthomcl: identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-2189, 2003.

F. Maumus, A. Epert, F. Nogue, and G. Blanc, Plant genomes enclose footprints of past infections by giant virus relatives, Nat. Commun, vol.5, p.4268, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204072

D. Moreira and C. Brochier-armanet, Giant viruses, giant chimeras: the multiple evolutionary histories of mimivirus genes, BMC Evol. Biol, vol.8, p.12, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00698068

A. Nasir, K. M. Kim, C. , and G. , Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms archaea, bacteria and eukarya, BMC Evol. Biol, vol.12, p.156, 2012.

N. Philippe, M. Legendre, G. Doutre, Y. Coute, O. Poirot et al., Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes, Science, vol.341, pp.281-286, 2013.
URL : https://hal.archives-ouvertes.fr/cea-00862677

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS ONE, vol.5, p.9490, 2010.

D. Raoult, Truc or the need for a new microbial classification, Intervirology, vol.56, pp.349-353, 2013.

D. Raoult, How the virophage compels the need to readdress the classification of microbes, Virology, vol.477, pp.119-124, 2014.

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-megabase genome sequence of mimivirus, Science, vol.306, pp.1344-1350, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

D. Raoult, F. , and P. , Redefining viruses: lessons from mimivirus, Nat. Rev. Microbiol, vol.6, pp.315-319, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00297223

D. Raoult, L. Scola, B. Birtles, and R. , The discovery and characterization of mimivirus, the largest known virus and putative pneumonia agent, Clin. Infect. Dis, vol.45, pp.95-102, 2007.

A. I. Saeed, V. Sharov, J. White, J. Li, W. Liang et al., Tm4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, pp.374-378, 2003.

V. Sharma, P. Colson, O. Chabrol, P. Scheid, P. Pontarotti et al., Welcome to pandoraviruses at the "fourth truc, club. Front. Microbiol, vol.6, p.423, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01211489

V. Sharma, P. Colson, R. Giorgi, P. Pontarotti, R. et al., , 2014.

, DNA-dependent RNA polymerase detects hidden giant viruses in published databanks, Genome Biol. Evol, vol.6

R. L. Tatusov, N. D. Fedorova, J. D. Jackson, A. R. Jacobs, B. Kiryutin et al., The cog database: an updated version includes eukaryotes, BMC Bioinformatics, vol.4, p.41, 2003.

T. A. Williams, T. M. Embley, H. , and E. , Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses, PLoS ONE, vol.6, p.21080, 2011.

C. R. Woese, O. Kandler, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya, Proc. Natl. Acad. Sci. U.S.A, vol.87, pp.4576-4579, 1990.

Y. I. Wolf, I. B. Rogozin, N. V. Grishin, and E. V. Koonin, Genome trees and the tree of life, Trends Genet, vol.18, pp.472-479, 2002.

D. Wu, M. Wu, A. Halpern, D. B. Rusch, S. Yooseph et al., Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees, PLoS ONE, vol.6, p.18011, 2011.

N. Yoosuf, N. Yutin, P. Colson, S. A. Shabalina, I. Pagnier et al., Related giant viruses in distant locations and different habitats: acanthamoeba polyphaga moumouvirus represents a third lineage of the mimiviridae that is close to the megavirus lineage, Genome Biol. Evol, vol.4, 2012.

N. Yutin and E. V. Koonin, Evolution of DNA ligases of nucleocytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity, Biol. Direct, vol.4, p.51, 2009.

N. Yutin and E. V. Koonin, Hidden evolutionary complexity of nucleocytoplasmic large DNA viruses of eukaryotes, Virol. J, vol.9, p.161, 2012.

N. Yutin, Y. I. Wolf, and E. V. Koonin, Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life, Virology, vol.466, pp.38-52, 2014.

N. Yutin, Y. I. Wolf, D. Raoult, and E. V. Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution, Virol. J, vol.17, p.223, 2009.

, Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest

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