L. Iyer, L. Aravind, and E. Koonin, Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses, Journal of Virology, vol.75, issue.23, pp.7511720-11734, 2001.
DOI : 10.1128/JVI.75.23.11720-11734.2001

L. Iyer, S. Balaji, E. Koonin, and L. Aravind, Evolutionary genomics of nucleo-cytoplasmic large DNA viruses, Virus Research, vol.117, issue.1, pp.156-184, 2006.
DOI : 10.1016/j.virusres.2006.01.009

E. Koonin and N. Yutin, Origin and evolution of eukaryotic large nucleocytoplasmic DNA viruses, Intervirology, vol.2010, issue.535, pp.284-292

C. Netherton and T. Wileman, Virus factories, double membrane vesicles and viroplasm generated in animal cells, Current Opinion in Virology, vol.1, issue.5, pp.381-387, 2011.
DOI : 10.1016/j.coviro.2011.09.008

I. De-castro, L. Volonte, and C. Risco, Virus factories: biogenesis and structural design, Cellular Microbiology, vol.13, issue.1, pp.24-34
DOI : 10.1111/cmi.12029

J. Van-etten and D. Dunigan, Chloroviruses: not your everyday plant virus, Trends in Plant Science, vol.17, issue.1, pp.1-8
DOI : 10.1016/j.tplants.2011.10.005

J. Van-etten, Unusual Life Style of Giant Chlorella Viruses, Annual Review of Genetics, vol.37, issue.1, pp.153-195, 2003.
DOI : 10.1146/annurev.genet.37.110801.143915

N. Yutin, Y. Wolf, D. Raoult, and E. Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution, Virology Journal, vol.6, issue.1, p.223, 2009.
DOI : 10.1186/1743-422X-6-223

P. Colson, X. De-lamballerie, G. Fournous, and D. Raoult, Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales, Intervirology, vol.2012, issue.555, pp.321-332

B. Moss and P. Howley, Poxviridae: the viruses and their replication In Fields Virology, pp.2905-2946

J. Claverie and C. Abergel, Mimivirus: the emerging paradox of quasi-autonomous viruses, Trends in Genetics, vol.26, issue.10, pp.431-437, 2010.
DOI : 10.1016/j.tig.2010.07.003

J. Claverie, H. Ogata, S. Audic, C. Abergel, K. Suhre et al., Mimivirus and the emerging concept of ???giant??? virus, Virus Research, vol.117, issue.1, pp.133-144, 2006.
DOI : 10.1016/j.virusres.2006.01.008

URL : https://hal.archives-ouvertes.fr/hal-00005228

D. Raoult and P. Forterre, Redefining viruses: lessons from Mimivirus, Nature Reviews Microbiology, vol.79, issue.4, pp.315-319, 2008.
DOI : 10.1038/nrmicro1858

URL : https://hal.archives-ouvertes.fr/hal-00297223

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-Megabase Genome Sequence of Mimivirus, Science, vol.306, issue.5700, pp.3061344-1350, 2004.
DOI : 10.1126/science.1101485

URL : https://hal.archives-ouvertes.fr/hal-00651656

M. Suzan-monti, L. Scola, B. Raoult, and D. , Genomic and evolutionary aspects of Mimivirus, Virus Research, vol.117, issue.1, pp.145-155, 2005.
DOI : 10.1016/j.virusres.2005.07.011

L. Scola, B. Desnues, C. Pagnier, I. Robert, C. Barrassi et al., The virophage as a unique parasite of the giant mimivirus, Nature, vol.32, issue.7209, pp.455100-104, 2008.
DOI : 10.1038/nature07218

URL : https://hal.archives-ouvertes.fr/hal-00354651

P. Colson, N. Yutin, S. Shabalina, C. Robert, G. Fournous et al., Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes, Genome Biology and Evolution, vol.3, issue.0, pp.737-742, 2011.
DOI : 10.1093/gbe/evr048

N. Yoosuf, N. Yutin, P. Colson, S. 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 Biology and Evolution, vol.4, issue.12, pp.1324-1330
DOI : 10.1093/gbe/evs109

L. Scola, B. Campocasso, A. , N. Dong, R. Fournous et al., Tentative Characterization of New Environmental Giant Viruses by MALDI-TOF Mass Spectrometry, Intervirology, vol.53, issue.5, pp.344-353, 2010.
DOI : 10.1159/000312919

D. Arslan, M. Legendre, V. Seltzer, C. Abergel, and J. Claverie, Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proceedings of the National Academy of Sciences, vol.108, issue.42, pp.17486-17491, 2011.
DOI : 10.1073/pnas.1110889108

M. Fischer, M. Allen, W. Wilson, and C. Suttle, Giant virus with a remarkable complement of genes infects marine zooplankton, Proceedings of the National Academy of Sciences, vol.107, issue.45, pp.19508-19513, 2010.
DOI : 10.1073/pnas.1007615107

J. Van-etten, Another Really, Really Big Virus, Viruses, vol.3, issue.12, pp.32-46, 2011.
DOI : 10.3390/v3010032

P. Colson, G. Gimenez, M. Boyer, G. Fournous, and D. Raoult, 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.29, issue.12, p.18935, 2011.
DOI : 10.1371/journal.pone.0018935.s016

A. Monier, J. Claverie, and H. Ogata, Taxonomic distribution of large DNA viruses in the sea, Genome Biology, vol.9, issue.7, p.106, 2008.
DOI : 10.1186/gb-2008-9-7-r106

A. Monier, J. Larsen, R. Sandaa, G. Bratbak, J. Claverie et al., Marine mimivirus relatives are probably large algal viruses, Virology Journal, vol.5, issue.1, p.12, 2008.
DOI : 10.1186/1743-422X-5-12

T. Williams, T. Embley, and E. Heinz, Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses, PLoS ONE, vol.51, issue.6, p.21080, 2011.
DOI : 10.1371/journal.pone.0021080.s010

M. Legendre, D. Arslan, C. Abergel, and J. Claverie, Genomics of Megavirus and the elusive fourth domain of Life, Communicative & Integrative Biology, vol.5, issue.1, pp.102-106
DOI : 10.1186/1471-2164-8-456

A. Nasir, K. Kim, and G. Caetano-anolles, Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya, BMC Evolutionary Biology, vol.12, issue.1, p.156
DOI : 10.1074/jbc.C111.325795

C. Desnues, L. Scola, B. Yutin, N. Fournous, G. Robert et al., Provirophages and transpovirons as the diverse mobilome of giant viruses, Proceedings of the National Academy of Sciences, vol.109, issue.44, pp.18078-18083, 2012.
DOI : 10.1073/pnas.1208835109

C. Desnues, M. Boyer, and D. Raoult, Sputnik, a Virophage Infecting the Viral Domain of Life, Adv Virus Res, vol.82, pp.63-89, 2012.
DOI : 10.1016/B978-0-12-394621-8.00013-3

M. Fischer and C. Suttle, A Virophage at the Origin of Large DNA Transposons, Science, vol.332, issue.6026, pp.231-234
DOI : 10.1126/science.1199412

S. Yau, F. Lauro, M. Demaere, M. Brown, T. Thomas et al., Virophage control of antarctic algal host-virus dynamics, Proceedings of the National Academy of Sciences, vol.108, issue.15, pp.6163-6168, 2011.
DOI : 10.1073/pnas.1018221108

A. Baudoux and C. Brussaard, Characterization of different viruses infecting the marine harmful algal bloom species Phaeocystis globosa, Virology, vol.341, issue.1, pp.80-90, 2005.
DOI : 10.1016/j.virol.2005.07.002

C. Brussard, G. Bratbak, A. Baudoux, and P. Ruardij, Phaeocystis and its interaction with viruses, Biogeochemistry, vol.79, issue.1-3, pp.201-215, 2007.
DOI : 10.1007/s10533-007-9096-0

R. Tatusov, E. Koonin, and D. Lipman, A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.631-637, 1997.
DOI : 10.1126/science.278.5338.631

D. Kristensen, Y. Wolf, A. Mushegian, and E. Koonin, Computational methods for Gene Orthology inference, Briefings in Bioinformatics, vol.12, issue.5, pp.379-391, 2011.
DOI : 10.1093/bib/bbr030

D. Kristensen, L. Kannan, M. Coleman, Y. Wolf, A. Sorokin et al., Mushegian A: A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches, Bioinformatics, issue.12, pp.261481-1487, 2010.

N. Yutin and E. Koonin, Proteorhodopsin genes in giant viruses, Biology Direct, vol.7, issue.1, p.34, 2012.
DOI : 10.1006/jmbi.2000.4315

Y. Wolf, I. Rogozin, N. Grishin, R. Tatusov, and E. Koonin, Genome trees constructed using five different approaches suggest new major bacterial clades, BMC Evolutionary Biology, vol.1, issue.1, p.8, 2001.
DOI : 10.1186/1471-2148-1-8

N. Yutin and E. Koonin, Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes, Virology Journal, vol.9, issue.1, p.161
DOI : 10.1186/1743-422X-9-161

M. Csuros, Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood, Bioinformatics, vol.2010, issue.2615, pp.1910-1912

P. Colson and D. Raoult, Gene Repertoire of Amoeba-Associated Giant Viruses, Intervirology, vol.53, issue.5, pp.330-343
DOI : 10.1159/000312918

G. Greub and D. Raoult, Microorganisms Resistant to Free-Living Amoebae, Clinical Microbiology Reviews, vol.17, issue.2, pp.413-433, 2004.
DOI : 10.1128/CMR.17.2.413-433.2004

D. Raoult and M. Boyer, Amoebae as Genitors and Reservoirs of Giant Viruses, Intervirology, vol.53, issue.5, pp.321-329
DOI : 10.1159/000312917

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, Proceedings of the National Academy of Sciences, vol.106, issue.51, pp.10621848-21853, 2009.
DOI : 10.1073/pnas.0911354106

J. Zhou, W. Zhang, S. Yan, X. J. Zhang, Y. Li et al., Diversity of Virophages in Metagenomic Data Sets, Journal of Virology, vol.87, issue.8, pp.4225-4236, 2013.
DOI : 10.1128/JVI.03398-12

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

A. Marchler-bauer and S. Bryant, CD-Search: protein domain annotations on the fly, Nucleic Acids Research, vol.32, issue.Web Server, pp.327-331, 2004.
DOI : 10.1093/nar/gkh454

J. Felsenstein, [24] Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods, Methods Enzymol, vol.266, pp.418-427, 1996.
DOI : 10.1016/S0076-6879(96)66026-1

N. Yutin, K. Makarova, S. Mekhedov, Y. Wolf, and E. Koonin, The Deep Archaeal Roots of Eukaryotes, Molecular Biology and Evolution, vol.25, issue.8, pp.251619-1630, 2008.
DOI : 10.1093/molbev/msn108

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

D. Darriba, G. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1165, 2011.
DOI : 10.1093/bioinformatics/btr088

G. Jobb, A. Von-haeseler, and K. Strimmer, TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics, BMC Evolutionary Biology, vol.4, issue.1, p.18, 2004.
DOI : 10.1186/1471-2148-4-18

H. Shimodaira, An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002.
DOI : 10.1080/10635150290069913