R. A. Edwards and . Rohwer, Viral metagenomics, Nat. Rev. Microbiol, vol.3, pp.504-510, 2005.

F. Rohwer, Global phage diversity, Cell, vol.113, p.141, 2003.
DOI : 10.1016/s0092-8674(03)00276-9

URL : https://doi.org/10.1016/s0092-8674(03)00276-9

C. A. Suttle, Marine viruses: major players in the global ecosystem, Nat. Rev. Microbiol, vol.5, pp.801-812, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01663342

E. V. Koonin and . Dolja, A virocentric perspective on the evolution of life, Curr. Opin. Virol, vol.3, pp.546-557, 2013.

M. D. Krupovic and . Bamford, Order to the viral universe, J. Virol, vol.84, pp.12476-12479, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01977412

E. V. Koonin and . Dolja, Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol, Mol. Biol. Rev, vol.78, pp.278-303, 2014.

D. M. Kristensen, Orthologous gene clusters and taxon signature genes for viruses of prokaryotes, J. Bacteriol, vol.195, pp.941-950, 2013.

E. V. Koonin, T. G. Senkevich-&-v, and . Dolja, The ancient Virus World and evolution of cells, Biol. Direct, vol.1, p.29, 2006.

E. C. Holmes, What does virus evolution tell us about virus origins?, J. Virol, vol.85, pp.5247-5251, 2011.
DOI : 10.1128/jvi.02203-10

URL : https://jvi.asm.org/content/85/11/5247.full.pdf

E. V. Koonin, On the origin of cells and viruses: primordial virus world scenario, Ann. N. Y. Acad. Sci, vol.1178, pp.47-64, 2009.

M. Krupovic, Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol, Mol. Biol. Rev, vol.75, pp.610-635, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01977409

H. H. Kazazian and . Jr, Mobile elements: drivers of genome evolution, Science, vol.303, pp.1626-1632, 2004.

J. L. Goodier and H. H. Kazazian, Retrotransposons revisited: the restraint and rehabilitation of parasites, Cell, vol.135, pp.23-35, 2008.

D. Raoult, The 1.2-megabase genome sequence of Mimivirus, Science, vol.306, pp.1344-1350, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

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

N. Philippe, Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes, Science, vol.341, pp.281-286, 2013.
DOI : 10.1126/science.1239181

URL : https://hal.archives-ouvertes.fr/cea-00862677

M. Legendre, 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.

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

L. M. Iyer, Evolutionary genomics of nucleocytoplasmic large DNA viruses, Virus Res, vol.117, pp.156-184, 2006.

P. Colson, 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

L. Scola and B. , The virophage as a unique parasite of the giant mimivirus, Nature, vol.455, pp.100-104, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00354651

J. M. Claverie and . Abergel, Mimivirus and its virophage, Annu. Rev. Genet, vol.43, pp.49-66, 2009.
DOI : 10.1146/annurev-genet-102108-134255

C. Desnues, M. Boyer, and &. Raoult, Sputnik, a virophage infecting the viral domain of life, Adv. Virus Res, vol.82, pp.63-89, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02008679

M. &. Krupovic and . Cvirkaite-krupovic, Virophages or satellite viruses?, Nat. Rev. Microbiol, vol.9, pp.762-763, 2011.
DOI : 10.1038/nrmicro2676

URL : https://hal.archives-ouvertes.fr/pasteur-01977410

M. G. Fischer and C. A. Suttle, A virophage at the origin of large DNA transposons, Science, vol.332, pp.231-234, 2011.

N. Yutin, D. &. Raoult, and . Koonin, Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies, Virol. J, vol.10, p.158, 2013.

M. Krupovic, D. H. Bamford, and &. E. Koonin, Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses, Biol. Direct, vol.9, p.6, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-00994115

M. E. Krupovic and . Koonin, Polintons: the hotbed of eukaryotic virus, transposon and plasmid evolution, Nat. Rev. Microbiol, vol.13, pp.105-115, 2015.

V. V. Kapitonov and . Jurka, Self-synthesizing DNA transposons in eukaryotes, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.4540-4545, 2006.

E. J. Pritham, T. Putliwala, and &. Feschotte, Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses, Gene, vol.390, pp.3-17, 2007.

J. Jurka, Repetitive sequences in complex genomes: structure and evolution, Annu. Rev. Genomics Hum. Genet, vol.8, pp.241-259, 2007.
DOI : 10.1146/annurev.genom.8.080706.092416

, The Authors. Annals of the New York Academy of Sciences, vol.1341, pp.10-24, 2015.

M. E. Krupovic and . Koonin, Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses, Sci. Rep, vol.4, p.5347, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01977398

W. Bao, V. V. Kapitonov, and J. Jurka, Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons, Mob. DNA, vol.1, p.3, 2010.
DOI : 10.1186/1759-8753-1-3

URL : https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/1759-8753-1-3

A. &. Gillis and . Mahillon, Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future, Viruses, vol.6, pp.2623-2672, 2014.
DOI : 10.3390/v6072623

URL : http://www.mdpi.com/1999-4915/6/7/2623/pdf

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

S. B. Sandmeyer and . Menees, Morphogenesis at the retrotransposon-retrovirus interface: gypsy and copia families in yeast and Drosophila, Curr. Top Microbiol. Immunol, vol.214, pp.261-296, 1996.

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

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

Y. J. Wang and . Jehle, Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: new insights on an old topic, J. Invertebr. Pathol, vol.101, pp.187-193, 2009.
DOI : 10.1016/j.jip.2009.03.013

J. A. Jehle, A. M. Abd-alla, and &. Y. Wang, Phylogeny and evolution of Hytrosaviridae, J. Invertebr. Pathol, vol.112, pp.62-67, 2013.

J. Theze, Paleozoic origin of insect large dsDNA viruses, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.15931-15935, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00659590

Y. Wang, O. R. Bininda-emonds, and &. J. Jehle, Nudivirus genomics and phylogeny, Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions. M. Garcia, pp.33-52, 2012.

S. Selvarajan-sigamani, The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses, J. Virol, vol.87, pp.7140-7148, 2013.

M. K. Pietilä, Structure of the archaeal headtailed virus HSTV-1 completes the HK97 fold story, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.10604-10609, 2013.

F. J. Rixon and . Schmid, Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages, Curr. Opin. Virol, vol.5, pp.105-110, 2014.

M. D. Krupovic and . Bamford, Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly, Curr. Opin. Virol, vol.1, pp.118-124, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01977407

T. V. Ilyina and . Koonin, Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria, Nucleic Acids Res, vol.20, pp.3279-3285, 1992.

L. M. Iyer, Origin and evolution of the archaeoeukaryotic primase superfamily and related palm-domain proteins: structural insights and new members, Nucleic Acids Res, vol.33, pp.3875-3896, 2005.

M. Krupovic, Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Curr. Opin. Virol, vol.3, pp.578-586, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01977403

L. Scola and B. , A giant virus in amoebae, Science, vol.299, p.2033, 2003.

E. V. Koonin, Virology: Gulliver among the Lilliputians, Curr. Biol, vol.15, pp.167-169, 2005.

J. M. Claverie, Mimivirus and the emerging concept of "giant, virus. Virus Res, vol.117, pp.133-144, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00005228

J. L. Van-etten, Another really, really big virus, Viruses, vol.3, pp.32-46, 2011.

J. L. Van-etten, L. C. Lane-&-d, and . Dunigan, DNA viruses: the really big ones (giruses), Annu. Rev. Microbiol, vol.64, pp.83-99, 2010.

P. Colson, Viruses with more than 1000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes, Genome Biol. Evol, vol.3, pp.737-742, 2011.

N. Yoosuf, 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, pp.1324-1330, 2012.

M. Legendre, Genomics of Megavirus and the elusive fourth domain of Life, Commun. Integr. Biol, vol.5, pp.102-106, 2012.

P. Forterre, M. &. Krupovic, and . Prangishvili, Cellular domains and viral lineages, Trends Microbiol, vol.22, pp.554-558, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01977393

C. R. Woese, Bacterial evolution, Microbiol. Rev, vol.51, pp.221-271, 1987.

C. R. Woese and . Fox, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proc. Natl. Acad. Sci. U.S.A, vol.74, pp.5088-5090, 1977.

C. R. Woese, O. &. Kandler, and . 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.

C. R. Woese, L. J. Magrum-&-g, and . Fox, Archaebacteria. J. Mol. Evol, vol.11, pp.245-251, 1978.

N. R. Pace, A molecular view of microbial diversity and the biosphere, Science, vol.276, pp.734-740, 1997.

N. R. Pace, Time for a change, Nature, vol.441, p.289, 2006.

J. R. Brown and . Doolittle, Archaea and the prokaryote-to-eukaryote transition, Microbiolm Molm Biolm Rev, vol.61, pp.456-502, 1997.

J. R. Brown, Genomic and phylogenetic perspectives on the evolution of prokaryotes, Syst. Biol, vol.50, pp.497-512, 2001.

P. Puigbo, Y. I. Wolf-&-e, and . Koonin, Search for a 'Tree of Life' in the thicket of the phylogenetic forest, J. Biol, vol.8, p.59, 2009.

P. Colson, Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales, Intervirology, vol.55, pp.321-332, 2012.

P. Colson, 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, p.18935, 2011.

A. Nasir, K. M. Kim, and &. Caetano-anolles, Giant viruses coexisted with the cellular ancestors and represent 23, 2012.

, The Authors, vol.1341, pp.10-24, 2015.

, on behalf of The New York Academy of Sciences. a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya, vol.12, p.156

J. Felsenstein, Inferring Phylogenies, 2004.

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

L. M. Iyer, Evolutionary genomics of nucleocytoplasmic large DNA viruses, Virus Res, vol.117, pp.156-184, 2006.

N. Yutin, Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution, Virol. J, vol.6, p.223, 2009.

N. Yutin, Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family, Virol. J, vol.10, p.106, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-00808995

S. Santini, Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.10800-10805, 2013.

N. E. Yutin and . Koonin, Pandoraviruses are highly derived phycodnaviruses, Biol. Direct, vol.8, p.25, 2013.

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

M. D. Krupovic and . Bamford, Virus evolution: how far does the double beta-barrel viral lineage extend?, Nat. Rev. Microbiol, vol.6, pp.941-948, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-01977417

T. M. Embley and . Martin, Eukaryotic evolution, changes and challenges, Nature, vol.440, pp.623-630, 2006.
DOI : 10.1038/nature04546

URL : https://zenodo.org/record/897869/files/article.pdf

W. E. Martin and . Koonin, Introns and the origin of nucleus-cytosol compartmentation, Nature, vol.440, pp.41-45, 2006.

, The Authors. Annals of the New York Academy of Sciences, vol.1341, pp.10-24, 2015.