K. E. Wommack and R. R. Colwell, Virioplankton: viruses in aquatic ecosystems, Microbiol Mol Biol Rev, vol.64, pp.69-114, 2000.

C. A. Suttle, Marine viruses-major players in the global ecosystem, Nat Rev Microbiol, vol.5, pp.801-813, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01663342

J. M. Rowe, J. M. Debruyn, L. Poorvin, G. R. Lecleir, Z. I. Johnson et al., Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms, FEMS Microbiol Ecol, vol.79, pp.359-70, 2012.

C. H. Wigington, D. Sonderegger, C. Brussaard, A. Buchan, J. F. Finke et al., Re-examination of the relationship between marine virus and microbial cell abundances, Nat Microbiol, vol.1, p.15024, 2016.

F. Schulz, L. Alteio, D. Goudeau, E. M. Ryan, F. B. Yu et al., Hidden diversity of soil giant viruses, Nat Commun, vol.9, p.4881, 2018.

S. R. Abeles and D. T. Pride, Molecular bases and role of viruses in the human microbiome, J Mol Biol, vol.426, pp.3892-906, 2014.

J. J. Barr, A bacteriophages journey through the human body, Immunol Rev, vol.279, pp.106-128, 2017.

E. Atoni, Y. Wang, S. Karungu, C. Waruhiu, A. Zohaib et al., Metagenomic virome analysis of culex mosquitoes from Kenya and China, Viruses, vol.10, p.30, 2018.

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

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-megabase genome sequence of Mimivirus, Science, vol.306, pp.1344-50, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

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.281-287, 2013.
URL : https://hal.archives-ouvertes.fr/cea-00862677

, Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of

M. Legendre, A. Lartigue, L. Bertaux, S. Jeudy, J. Bartoli et al., In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba, Proc Natl Acad Sci, vol.112, pp.5327-5362, 2015.
URL : https://hal.archives-ouvertes.fr/cea-01825900

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, vol.111, pp.4274-4283, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02193478

W. H. Wilson, D. C. Schroeder, M. J. Allen, M. Holden, J. Parkhill et al., Complete genome sequence and lytic phase transcription profile of a Coccolithovirus, Science, vol.309, pp.1090-1092, 2005.

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 USA, vol.107, pp.19508-19521, 2010.

S. Santini, S. Jeudy, J. Bartoli, O. Poirot, M. Lescot et al., Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes, Proc Natl Acad Sci, vol.110, pp.10800-10805, 2013.

L. Gallot-lavallée, G. Blanc, and J. Claverie, Comparative genomics of Chrysochromulina ericina virus and other microalga-infecting large DNA viruses highlights their intricate evolutionary relationship with the established Mimiviridae family, J Virol, vol.91, pp.230-247, 2017.

C. M. Deeg, C. Chow, and C. A. Suttle, The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea, vol.7, 2017.

U. Sheyn, S. Rosenwasser, Y. Lehahn, N. Barak-gavish, R. Rotkopf et al., Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export, ISME J, vol.12, pp.704-717, 2018.

D. Arslan, M. Legendre, V. Seltzer, C. Abergel, and J. Claverie, Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proc Natl Acad Sci USA, vol.108, pp.17486-91, 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, pp.1324-1354, 2012.

N. Yoosuf, I. Pagnier, G. Fournous, C. Robert, L. Scola et al., Complete genome sequence of Courdo11 virus, a member of the family Mimiviridae, Virus Genes, vol.48, pp.218-241, 2014.

J. Claverie and C. Abergel, Mimiviridae: an expanding family of highly diverse large dsDNA viruses infecting a wide phylogenetic range of aquatic eukaryotes, Viruses, vol.10, p.506, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01887346

F. Schulz, N. Yutin, N. N. Ivanova, D. R. Ortega, T. K. Lee et al., Giant viruses with an expanded complement of translation system components, Science, vol.356, pp.82-87, 2017.

L. Scola, B. Desnues, C. Pagnier, I. Robert, C. Barrassi et al., 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

C. Desnues, L. Scola, B. Yutin, N. Fournous, G. Robert et al., Provirophages and transpovirons as the diverse mobilome of giant viruses, Proc Natl Acad Sci, vol.109, pp.18078-83, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02007283

M. Gaia, I. Pagnier, A. Campocasso, G. Fournous, D. Raoult et al., Broad spectrum of mimiviridae virophage allows its isolation using a Mimivirus reporter, PloS ONE, vol.8, p.61912, 2013.

M. Gaia, S. Benamar, M. Boughalmi, I. Pagnier, O. Croce et al., Zamilon, a novel virophage with Mimiviridae host specificity, PloS ONE, vol.9, p.94923, 2014.

M. Krupovic, J. H. Kuhn, and M. G. Fischer, A classification system for virophages and satellite viruses, Arch Virol, vol.161, pp.233-280, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977384

M. Bekliz, P. Colson, L. Scola, and B. , The expanding family of virophages, Viruses, vol.8, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453275

M. G. Fischer and C. A. Suttle, A virophage at the origin of large DNA transposons, Science, vol.332, pp.231-235, 2011.

M. G. Fischer and T. Hackl, Host genome integration and giant virusinduced reactivation of the virophage mavirus, Nature, vol.540, pp.288-91, 2016.

A. Levasseur, M. Bekliz, E. Chabrière, P. Pontarotti, L. Scola et al., MIMIVIRE is a defence system in Mimivirus that confers resistance to virophage, Nature, vol.531, pp.249-52, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01306166

J. Claverie and C. Abergel, CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system, Virol Sin, vol.31, pp.193-199, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01768356

S. Mougari, J. Abrahao, G. P. Oliveira, B. Khalil, J. Y. et al., Role of the R349 gene and its repeats in the MIMIVIRE defense system, Front Microbiol, vol.10, p.1147, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02243367

E. Fabre, S. Jeudy, S. Santini, M. Legendre, M. Trauchessec et al., Noumeavirus replication relies on a transient remote control of the host nucleus, Nat Commun, vol.8, p.15087, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01534406

C. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake et al., finished microbial genome assemblies from long-read SMRT sequencing data, Nat Methods, vol.10, pp.563-572, 2013.

S. Nurk, A. Bankevich, D. Antipov, A. Gurevich, A. Korobeynikov et al., Assembling single-cell genomes and minimetagenomes from chimeric MDA products, J Comput Biol, vol.20, pp.714-751, 2013.

M. Stanke and S. Waack, Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, vol.19, issue.Suppl_2, pp.215-240, 2003.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-64, 1997.

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.403-413, 1990.

A. Marchler-bauer, Y. Bo, L. Han, J. He, C. J. Lanczycki et al., CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017.

D. Darriba, G. L. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinforma Oxf Engl, vol.27, pp.1164-1169, 2011.

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-84, 2002.

I. M. Wallace, O. O'sullivan, D. G. Higgins, and C. Notredame, M-Coffee: combining multiple sequence alignment methods with T-Coffee, Nucleic Acids Res, vol.34, pp.1692-1701, 2006.

S. Yoon, S. Ha, J. Lim, S. Kwon, and J. Chun, A large-scale evaluation of algorithms to calculate average nucleotide identity

, Antonie Van Leeuwenhoek, vol.110, pp.1281-1287, 2017.

J. Cox and M. Mann, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification, Nat Biotechnol, vol.26, pp.1367-72, 2008.

B. Schwanhäusser, D. Busse, N. Li, G. Dittmar, J. Schuchhardt et al., Global quantification of mammalian gene expression control, Nature, vol.473, pp.337-379, 2011.

J. Shin, J. F. Krey, A. Hassan, Z. Metlagel, A. N. Tauscher et al., Molecular architecture of the chick vestibular hair bundle, Nat Neurosci, vol.16, pp.365-74, 2013.

N. Zauberman, Y. Mutsafi, D. B. Halevy, E. Shimoni, E. Klein et al., Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga Mimivirus, PLoS Biol, vol.6, p.114, 2008.

J. Abrahão, L. Silva, L. S. Silva, J. Khalil, R. Rodrigues et al., Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere, Nat Commun, vol.9, p.749, 2018.

A. Andrade, R. Rodrigues, G. P. Oliveira, K. R. Andrade, C. A. Bonjardim et al., Filling knowledge gaps for Mimivirus entry, uncoating, and morphogenesis, J Virol, vol.91, pp.1335-1352, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01730467

J. Claverie and C. Abergel, Mimivirus and its virophage, Annu Rev Genet, vol.43, pp.49-66, 2009.

N. Yoosuf, I. Pagnier, G. Fournous, C. Robert, D. Raoult et al., Draft genome sequences of Terra1 and Terra2 viruses, new members of the family Mimiviridae isolated from soil. Virology, pp.125-157, 2014.

M. Krupovic, N. Yutin, and E. V. Koonin, Fusion of a superfamily 1 helicase and an inactivated DNA polymerase is a signature of common evolutionary history of Polintons, polinton-like viruses, Tlr1 transposons and transpovirons, Virus Evol, vol.2, p.19, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977355

D. Byrne, R. Grzela, A. Lartigue, S. Audic, S. Chenivesse et al., The polyadenylation site of Mimivirus transcripts obeys a stringent "hairpin rule, Genome Res, vol.19, pp.1233-1275, 2009.

M. Legendre, S. Audic, O. Poirot, P. Hingamp, V. Seltzer et al., mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus, Genome Res, vol.20, pp.664-74, 2010.

M. Legendre, S. Santini, A. Rico, C. Abergel, and J. Claverie, Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing, Virol J, vol.8, p.99, 2011.

S. Priet, A. Lartigue, F. Debart, J. Claverie, and C. Abergel, mRNA maturation in giant viruses: variation on a theme, Nucleic Acids Res, vol.43, pp.3776-88, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01768294

R. P. Novick, Extrachromosomal inheritance in bacteria, Bacteriol Rev, vol.33, pp.210-63, 1969.

R. P. Novick, Plasmid incompatibility. Microbiol Rev, vol.51, pp.381-95, 1987.

M. P. Garcillán-barcia and F. De-la-cruz, Why is entry exclusion an essential feature of conjugative plasmids?, Plasmid, vol.60, pp.1-18, 2008.

M. Humbert, K. T. Huguet, F. Coulombe, and V. Burrus, Entry exclusion of conjugative plasmids of the IncA, IncC and related untyped incompatibility groups, J Bacteriol, vol.201, pp.731-749, 2019.

M. K. Donnelly-wu, W. R. Jacobs, and G. F. Hatfull, Superinfection immunity of mycobacteriophage L5: applications for genetic transformation of mycobacteria, Mol Microbiol, vol.7, pp.407-424, 1993.

M. M. Susskind, A. Wright, and D. Botstein, Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. IV. Genetics and physiology of sieB exclusion, Virology, vol.62, pp.367-84, 1974.

S. Mcgrath, G. F. Fitzgerald, and D. Van-sinderen, Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages, Mol Microbiol, vol.43, pp.509-529, 2002.

J. Mahony, S. Mcgrath, G. F. Fitzgerald, and D. Van-sinderen, Identification and characterization of lactococcal-prophage-carried superinfection exclusion genes, Appl Environ Microbiol, vol.74, pp.6206-6221, 2008.

X. Sun, A. Göhler, K. J. Heller, and H. Neve, The ltp gene of temperate Streptococcus thermophilus phage TP-J34 confers superinfection exclusion to Streptococcus thermophilus and Lactococcus lactis, Virology, vol.350, pp.146-57, 2006.

I. A. Borges, . De-assisfl, . Silva, and J. Abrahão, Rio Negro virophage: sequencing of the near complete genome and transmission electron microscopy of viral factories and particles

, Braz J Microbiol Publ Braz Soc Microbiol, vol.49, issue.1, pp.260-261, 2018.

S. R. Parratt and A. Laine, The role of hyperparasitism in microbial pathogen ecology and evolution, ISME J, vol.10, pp.1815-1837, 2016.

S. Duponchel and M. G. Fischer, Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses, PLoS Pathog, vol.15, p.1007592, 2019.

S. Yau, F. M. Lauro, M. Z. Demaere, M. V. Brown, T. Thomas et al., Virophage control of antarctic algal host-virus dynamics, Proc Natl Acad Sci USA, vol.108, pp.6163-6171, 2011.

D. Wilkins, S. Yau, T. J. Williams, M. A. Allen, M. V. Brown et al., Key microbial drivers in Antarctic aquatic environments, FEMS Microbiol Rev, vol.37, pp.303-338, 2013.

J. Zhou, D. Sun, A. Childers, T. R. Mcdermott, Y. Wang et al., Three novel virophage genomes discovered from Yellowstone Lake metagenomes, J Virol, vol.89, pp.1278-85, 2015.

J. A. Vizcaíno, A. Csordas, N. Del-toro, J. A. Dianes, J. Griss et al., 2016 update of the PRIDE database and its related tools, Nucleic Acids Res, vol.44, p.11033, 2016.