R. A. Edwards and F. Rohwer, Viral metagenomics, Nat Rev Microbiol, vol.3, issue.6, pp.504-514, 2005.

F. Rohwer and R. V. Thurber, Viruses manipulate the marine environment, Nature, vol.459, issue.7244, pp.207-219, 2009.

D. M. Kristensen, A. R. Mushegian, V. V. Dolja, and E. V. Koonin, New dimensions of the virus world discovered through metagenomics, Trends Microbiol, vol.18, issue.1, pp.11-20, 2010.

K. Rosario and M. Breitbart, Exploring the viral world through metagenomics, Curr Opin Virol, vol.1, issue.4, pp.289-97, 2011.

C. M. Mizuno, F. Rodriguez-valera, N. E. Kimes, and R. Ghai, Expanding the marine virosphere using metagenomics, PLoS Genet, vol.9, issue.12, p.1003987, 2013.

P. Simmonds, Methods for virus classification and the challenge of incorporating metagenomic sequence data, J Gen Virol, vol.96, pp.1193-206, 2015.

P. Simmonds, M. J. Adams, M. Benko, M. Breitbart, J. R. Brister et al., Consensus statement: virus taxonomy in the age of metagenomics, Nat Rev Microbiol, vol.15, issue.3, pp.161-169, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977366

B. E. Dutilh, Metagenomic ventures into outer sequence space, Bacteriophage, vol.4, issue.4, p.979664, 2014.

B. E. Dutilh, N. Cassman, K. Mcnair, S. E. Sanchez, G. G. Silva et al., A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nat Commun, vol.5, p.4498, 2014.

C. Garcia-aljaro, E. Balleste, M. Muniesa, and J. Jofre, Determination of crAssphage in water samples and applicability for tracking human faecal pollution, Microb Biotechnol, vol.10, issue.6, pp.1775-80, 2017.

N. Yutin, K. S. Makarova, A. B. Gussow, M. Krupovic, A. Segall et al., Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut, Nat Microbiol, vol.3, issue.1, pp.38-46, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01977350

A. Philosof, N. Yutin, J. Flores-uribe, S. I. Koonin, E. V. Beja et al., Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota, Curr Biol, vol.27, issue.9, pp.1362-1370, 2017.

Y. Nishimura, H. Watai, T. Honda, T. Mihara, K. Omae et al., Environmental viral genomes shed new light on virus-host interactions in the ocean, mSphere, vol.2, issue.2, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01771841

K. Rosario, S. Duffy, and M. Breitbart, Diverse circovirus-like genome architectures revealed by environmental metagenomics, J Gen Virol, vol.90, pp.2418-2442, 2009.

S. Roux, F. Enault, G. Bronner, D. Vaulot, P. Forterre et al., Chimeric viruses blur the borders between the major groups of eukaryotic singlestranded DNA viruses, Nat Commun, vol.4, p.2700, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00881062

S. Roux, M. Krupovic, A. Poulet, D. Debroas, and F. Enault, Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads, PLoS One, vol.7, issue.7, p.40418, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00816089

K. Rosario, S. Duffy, and M. Breitbart, A field guide to eukaryotic circular singlestranded DNA viruses: insights gained from metagenomics, Arch Virol, vol.157, issue.10, pp.1851-71, 2012.

S. Roux, N. E. Solonenko, V. T. Dang, B. T. Poulos, S. M. Schwenck et al., Towards quantitative viromics for both double-stranded and single-stranded DNA viruses, PeerJ, vol.4, p.2777, 2016.

, Empty triangles denote direct repeats. Genes are shown by block arrows drawn to scale, Gene abbreviations: CRI, Phage replication protein

, MCP, major capsid protein; F1-F4, uncharacterized proteins; SSB, single-stranded DNA-binding protein

M. Krupovic, D. Prangishvili, R. W. Hendrix, and D. H. Bamford, Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere, Microbiol Mol Biol Rev, vol.75, issue.4, pp.610-645, 2011.
DOI : 10.1128/mmbr.00011-11

URL : https://hal.archives-ouvertes.fr/pasteur-01977409

M. Krupovic, Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Curr Opin Virol, vol.3, issue.5, pp.578-86, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01977403

E. V. Koonin, V. V. Dolja, and M. Krupovic, Origins and evolution of viruses of eukaryotes: the ultimate modularity, Virology, pp.479-480, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977389

M. Krupovic, Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses, BioEssays, vol.34, issue.10, pp.867-70, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01977405

M. Krupovic, N. Zhi, J. Li, G. Hu, E. V. Koonin et al., Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing, Genome Biol Evol, vol.7, issue.4, pp.993-1001, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977388

E. V. Koonin and V. V. Dolja, Virus world as an evolutionary network of viruses and capsidless selfish elements, Microbiol Mol Biol Rev, vol.78, issue.2, pp.278-303, 2014.

M. Krupovic and D. H. Bamford, Order to the viral universe, J Virol, vol.84, issue.24, pp.12476-12485, 2010.
DOI : 10.1128/jvi.01489-10

URL : https://hal.archives-ouvertes.fr/pasteur-01977412

M. Krupovic and E. V. Koonin, Multiple origins of viral capsid proteins from cellular ancestors, Proc Natl Acad Sci, vol.114, issue.12, pp.2401-2411, 2017.
DOI : 10.1073/pnas.1621061114

URL : https://hal.archives-ouvertes.fr/pasteur-01977364

J. Iranzo, M. Krupovic, and E. V. Koonin, The double-stranded DNA Virosphere as a modular hierarchical network of gene sharing, MBio, vol.7, issue.4, pp.978-994, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977375

A. M. Saren, J. J. Ravantti, S. D. Benson, R. M. Burnett, L. Paulin et al., A snapshot of viral evolution from genome analysis of the tectiviridae family, J Mol Biol, vol.350, issue.3, pp.427-467, 2005.

C. Y. Fu and J. E. Johnson, Structure and cell biology of archaeal virus STIV, Curr Opin Virol, vol.2, issue.2, pp.122-129, 2012.
DOI : 10.1016/j.coviro.2012.01.007

URL : http://europepmc.org/articles/pmc3322382?pdf=render

M. Krupovic and E. V. Koonin, Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat Rev Microbiol, vol.13, issue.2, pp.105-120, 2015.
DOI : 10.1038/nrmicro3389

URL : https://hal.archives-ouvertes.fr/pasteur-01977391

S. D. Benson, J. K. Bamford, D. H. Bamford, and R. M. Burnett, Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures, Cell, vol.98, issue.6, pp.825-858, 1999.
DOI : 10.1016/s0092-8674(00)81516-0

URL : https://doi.org/10.1016/s0092-8674(00)81516-0

S. D. Benson, J. K. Bamford, D. H. Bamford, and R. M. Burnett, Does common architecture reveal a viral lineage spanning all three domains of life?, Mol Cell, vol.16, issue.5, pp.673-85, 2004.
DOI : 10.1016/j.molcel.2004.11.016

URL : https://doi.org/10.1016/j.molcel.2004.11.016

L. M. Iyer, K. S. Makarova, E. V. Koonin, and L. Aravind, Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging, Nucleic Acids Res, vol.32, issue.17, pp.5260-79, 2004.

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf

, Database Resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.45, issue.D1, pp.12-19, 2017.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

URL : http://europepmc.org/articles/pmc390337?pdf=render

J. Soding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-60, 2005.
DOI : 10.1093/bioinformatics/bti125

URL : https://academic.oup.com/bioinformatics/article-pdf/21/7/951/749249/bti125.pdf

K. Zaremba-niedzwiedzka, E. F. Caceres, J. H. Saw, D. Backstrom, L. Juzokaite et al., Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, vol.541, issue.7637, pp.353-361, 2017.

S. R. Eddy, Accelerated profile HMM searches, PLoS Comput Biol, vol.7, issue.10, p.1002195, 2011.

S. Boisvert, F. Raymond, E. Godzaridis, F. Laviolette, and J. Corbeil, Ray Meta: scalable de novo metagenome assembly and profiling, Genome Biol, vol.13, issue.12, p.122, 2012.

M. Borodovsky and A. Lomsadze, Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite, Curr Protoc Microbiol, vol.32, pp.1-7, 2014.

A. Marchler-bauer, C. Zheng, F. Chitsaz, M. K. Derbyshire, L. Y. Geer et al., CDD: conserved domains and protein three-dimensional structure, Nucleic Acids Res, vol.41, pp.348-52, 2013.

T. Frickey and A. Lupas, CLANS: a java application for visualizing protein families based on pairwise similarity, Bioinformatics, vol.20, issue.18, pp.3702-3706, 2004.

N. Yutin, K. S. Makarova, S. L. Mekhedov, Y. I. Wolf, and E. V. Koonin, The deep archaeal roots of eukaryotes, Mol Biol Evol, vol.25, issue.8, pp.1619-1649, 2008.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximumlikelihood trees for large alignments, PLoS One, vol.5, issue.3, p.9490, 2010.

N. G. Abrescia, J. M. Grimes, H. M. Kivela, R. Assenberg, G. C. Sutton et al., Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2, Mol Cell, vol.31, issue.5, pp.749-61, 2008.

A. Spang, J. H. Saw, S. L. Jorgensen, K. Zaremba-niedzwiedzka, J. Martijn et al., Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, vol.521, issue.7551, pp.173-182, 2015.

L. M. Iyer, D. D. Leipe, E. V. Koonin, and L. Aravind, Evolutionary history and higher order classification of AAA+ ATPases, J Struct Biol, vol.146, issue.1-2, pp.11-31, 2004.

A. M. Burroughs, L. M. Lyer, and L. Aravind, Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems, Genome Dyn, vol.3, pp.48-65, 2007.

E. Laanto, S. Mantynen, D. Colibus, L. Marjakangas, J. Gillum et al., Virus found in a boreal lake links ssDNA and dsDNA viruses, Proc Natl Acad Sci, vol.114, issue.31, pp.8378-83, 2017.

M. Krupovic and D. H. Bamford, Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria, BMC Genomics, vol.8, p.236, 2007.
URL : https://hal.archives-ouvertes.fr/pasteur-01977423

H. M. Oksanen and C. Ictv-report, ICTV virus taxonomy profile: Corticoviridae, J Gen Virol, vol.98, issue.5, pp.888-897, 2017.

N. S. Atanasova, A. Sencilo, M. K. Pietila, E. Roine, H. M. Oksanen et al., Comparison of lipid-containing bacterial and archaeal viruses, Adv Virus Res, vol.92, pp.1-61, 2015.

M. Krupovic and D. H. Bamford, Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota, Virology, vol.375, issue.1, pp.292-300, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-01977420

M. Gaudin, M. Krupovic, E. Marguet, E. Gauliard, V. Cvirkaite-krupovic et al., Extracellular membrane vesicles harbouring viral genomes, Environ Microbiol, vol.16, issue.4, pp.1167-75, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01234212

E. Rensen, M. Krupovic, and D. Prangishvili, Mysterious hexagonal pyramids on the surface of Pyrobaculum cells, Biochimie, vol.118, pp.365-372, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977385

N. Dellas, J. C. Snyder, M. Dills, S. J. Nicolay, K. M. Kerchner et al., Structure-based mutagenesis of Sulfolobus turreted icosahedral virus B204 reveals essential residues in the Virionassociated DNA-packaging ATPase, J Virol, vol.90, issue.6, pp.2729-2768, 2015.

G. Rice, L. Tang, K. Stedman, F. Roberto, J. Spuhler et al., The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life, Proc Natl Acad Sci U S A, vol.101, issue.20, pp.7716-7736, 2004.

J. J. Ravantti, A. Gaidelyte, D. H. Bamford, and J. K. Bamford, Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage, Virology, vol.313, issue.2, pp.401-415, 2003.

S. Sozhamannan, M. Mckinstry, S. M. Lentz, M. Jalasvuori, F. Mcafee et al., Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity, Appl Environ Microbiol, vol.74, issue.21, pp.6792-6798, 2008.

S. Kan, N. Fornelos, R. Schuch, and V. A. Fischetti, Identification of a ligand on the Wip1 bacteriophage highly specific for a receptor on Bacillus anthracis, J Bacteriol, vol.195, pp.4355-64, 2013.

A. Gillis and J. Mahillon, Prevalence, genetic diversity, and host range of tectiviruses among members of the Bacillus cereus group, Appl Environ Microbiol, vol.80, issue.14, pp.4138-52, 2014.

M. Berjon-otero, A. Lechuga, J. Mehla, P. Uetz, M. Salas et al., Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins, J Virol, vol.91, pp.870-887, 2017.

M. Jalasvuori and K. Koskinen, Extending the hosts of Tectiviridae into four additional genera of gram-positive bacteria and more diverse Bacillus species, Virology, vol.518, pp.136-178, 2018.

J. J. Gill, B. Wang, E. Sestak, R. Young, and K. H. Chu, Characterization of a novel Tectivirus phage toil and its potential as an agent for biolipid extraction, Sci Rep, vol.8, issue.1, p.1062, 2018.

G. Amitai and R. Sorek, CRISPR-Cas adaptation: insights into the mechanism of action, Nat Rev Microbiol, vol.14, issue.2, pp.67-76, 2016.

S. H. Sternberg, H. Richter, E. Charpentier, and U. Qimron, Adaptation in CRISPR-Cas systems, Mol Cell, vol.61, issue.6, pp.797-808, 2016.

M. Krupovic, K. S. Makarova, P. Forterre, D. Prangishvili, and E. V. Koonin, Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol, vol.12, p.36, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01001796

M. Krupovic, P. Béguin, and E. V. Koonin, Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery, Curr Opin Microbiol, vol.38, pp.36-43, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977358

M. Krupovic, S. Shmakov, K. S. Makarova, P. Forterre, and E. V. Koonin, Recent mobility of Casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity, Genome Biol Evol, vol.8, issue.2, pp.375-86, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01443928

D. H. Bamford, J. Caldentey, and J. K. Bamford, Bacteriophage PRD1: a broad host range DSDNA tectivirus with an internal membrane, Adv Virus Res, vol.45, pp.281-319, 1995.

N. Yutin, S. Shevchenko, V. Kapitonov, M. Krupovic, and E. V. Koonin, A novel group of diverse Polinton-like viruses discovered by metagenome analysis, BMC Biol, vol.13, p.95, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977381

C. Philippe, M. Krupovic, F. Jaomanjaka, O. Claisse, M. Petrel et al., Bacteriophage GC1, a novel Tectivirus infecting Gluconobacter Cerinus, an acetic acid bacterium associated with wine-making, Viruses, vol.10, issue.1, p.39, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01977348

K. Holmfeldt, N. Solonenko, M. Shah, K. Corrier, L. Riemann et al., Twelve previously unknown phage genera are ubiquitous in global oceans, Proc Natl Acad Sci, vol.110, issue.31, pp.12798-803, 2013.

M. Krupovic, V. Cvirkaite-krupovic, J. Iranzo, D. Prangishvili, and E. V. Koonin, Viruses of archaea: structural, functional, environmental and evolutionary genomics, Virus Res, vol.244, pp.181-93, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01977349

V. V. Dolja and M. Krupovic, Accelerating expansion of the viral universe, Curr Opin Virol, vol.3, issue.5, pp.542-547, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01977402

K. M. Kauffman, F. A. Hussain, J. Yang, P. Arevalo, J. M. Brown et al., A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria, Nature, vol.554, issue.7690, pp.118-140, 2018.

V. Roitman-shemer, J. Stokrova, J. Forstova, and A. Oppenheim, Assemblages of simian virus 40 capsid proteins and viral DNA visualized by electron microscopy, Biochem Biophys Res Commun, vol.353, issue.2, pp.424-454, 2007.

C. Cerqueira and J. T. Schiller, Papillomavirus assembly: an overview and perspectives, Virus Res, vol.231, pp.103-110, 2017.

H. Zhang, C. Schwartz, D. Donatis, G. M. Guo, and P. , push through one-way valve" mechanism of viral DNA packaging, Adv Virus Res, vol.83, pp.415-65, 2012.

M. Krupovic and E. V. Koonin, Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Curr Opin Microbiol, vol.31, pp.25-33, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977380