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

M. Krupovic and D. H. Bamford, Order to the viral universe, J Virol, vol.84, issue.24, pp.12476-12485, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01977412

D. Raoult and P. Forterre, Redefining viruses: lessons from Mimivirus, Nat Rev Microbiol, vol.6, issue.4, pp.315-324, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00297223

P. Forterre, M. Krupovic, and D. Prangishvili, Cellular domains and viral lineages, Trends Microbiol, vol.22, issue.10, pp.554-562, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01977393

M. Jalasvuori and E. V. Koonin, Classification of prokaryotic genetic replicators: between selfishness and altruism, Ann N Y Acad Sci, vol.1341, pp.96-105, 2015.

M. Krupovic, D. H. Bamford, and E. V. Koonin, Conservation of major and minor jellyroll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses, Biol Direct, vol.9, issue.1, p.6, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-00994115

M. Jalasvuori, S. Mattila, and V. Hoikkala, Chasing the origin of viruses: capsidforming genes as a life-saving preadaptation within a community of early replicators, PLoS One, vol.10, issue.5, p.126094, 2015.

M. Krupovic and D. H. Bamford, Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly, Curr Opin Virol, vol.1, issue.2, pp.118-142, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01977407

M. Krupovic, E. R. Quemin, D. H. Bamford, P. Forterre, and D. Prangishvili, Unification of the globally distributed spindle-shaped viruses of the Archaea, J Virol, vol.88, issue.4, pp.2354-2362, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00951871

N. G. Abrescia, D. H. Bamford, J. M. Grimes, and D. I. Stuart, Structure unifies the viral universe, Annu Rev Biochem, vol.81, pp.795-822, 2012.

F. Dimaio, X. Yu, E. Rensen, M. Krupovic, D. Prangishvili et al., A virus that infects a hyperthermophile encapsidates A-form DNA, Science, vol.348, issue.6237, pp.914-921, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977386

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

D. Janekovic, S. Wunderl, I. Holz, W. Zillig, A. Gierl et al., TTV2 and TTV3, a family of viruses of the extremely thermophilic, anaerobic, sulfur reducing archaebacterium Thermoproteus tenax, Mol Gen Genet, vol.192, pp.39-45, 1983.

W. D. Reiter, W. Zillig, and P. Palm, Archaebacterial viruses, Adv Virus Res, vol.34, pp.143-88, 1988.

H. Neumann, V. Schwass, C. Eckerskorn, and W. Zillig, Identification and characterization of the genes encoding three structural proteins of the Thermoproteus tenax virus TTV1, Mol Gen Genet, vol.217, issue.1, pp.105-115, 1989.

H. Neumann and W. Zillig, Coat protein TP4 of the virus TTV1: primary structure of the gene and the protein, Nucleic Acids Res, vol.17, issue.22, p.9475, 1989.

D. Prangishvili and M. Krupovic, A new proposed taxon for double-stranded DNA viruses, the order "Ligamenvirales, Arch Virol, vol.157, issue.4, pp.791-796, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01977408

D. Prangishvili, Archaeal viruses: living fossils of the ancient virosphere, Ann N Y Acad Sci, vol.1341, pp.35-40, 2015.

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.

J. Söding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-60, 2005.

K. S. Makarova, D. H. Haft, R. Barrangou, S. J. Brouns, E. Charpentier et al., Evolution and classification of the CRISPR-Cas systems, Nat Rev Microbiol, vol.9, issue.6, pp.467-77, 2011.

K. S. Makarova, Y. I. Wolf, and E. V. Koonin, The basic building blocks and evolution of CRISPR-CAS systems, Biochem Soc Trans, vol.41, issue.6, pp.1392-400, 2013.

E. V. Koonin and M. Krupovic, Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nat Rev Genet, vol.16, issue.3, pp.184-92, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977392

E. V. Koonin and K. S. Makarova, CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes, RNA Biol, vol.10, issue.5, pp.679-86, 2013.

K. S. Makarova, L. Aravind, Y. I. Wolf, and E. V. Koonin, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems, Biol Direct, vol.6, p.38, 2011.

S. Lemak, N. Beloglazova, B. Nocek, T. Skarina, R. Flick et al., Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus, J Am Chem Soc, vol.135, issue.46, pp.17476-87, 2013.

S. Lemak, B. Nocek, N. Beloglazova, T. Skarina, R. Flick et al., The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity, Nucleic Acids Res, vol.42, issue.17, pp.11144-55, 2014.

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

Y. Guo, B. B. Kragelund, M. F. White, and X. Peng, Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities, J Mol Biol, vol.427, issue.12, pp.2179-91, 2015.

S. P. Hooton and I. F. Connerton, Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein, Front Microbiol, vol.5, p.744, 2014.

D. Prangishvili, E. V. Koonin, and M. Krupovic, Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea, Biochem Soc Trans, vol.41, issue.1, pp.443-50, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01977404

A. F. Gardner, D. Prangishvili, and W. E. Jack, Characterization of Sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease, Extremophiles, vol.15, issue.5, pp.619-643, 2011.

S. J. Gould and E. S. Vrba, Exaptation-a missing term in the science of form, Paleobiology, vol.8, issue.1, pp.4-15, 1982.

D. Kazlauskas and C. Venclovas, Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase, Bioinformatics, vol.30, issue.15, pp.2093-2100, 2014.

N. Yutin, G. Faure, E. V. Koonin, and A. R. Mushegian, Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase, Biol Direct, vol.9, issue.1, p.22, 2014.

J. Pei and N. V. Grishin, PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information, Methods Mol Biol, vol.1079, pp.263-71, 2014.

A. M. Waterhouse, J. B. Procter, D. M. Martin, M. Clamp, and G. J. Barton, Jalview Version 2-a multiple sequence alignment editor and analysis workbench, Bioinformatics, vol.25, issue.9, pp.1189-91, 2009.

M. A. Marti-renom, A. C. Stuart, A. Fiser, R. Sanchez, F. Melo et al., Comparative protein structure modeling of genes and genomes, Annu Rev Biophys Biomol Struct, vol.29, pp.291-325, 2000.

M. Wiederstein and M. J. Sippl, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res, vol.35, pp.407-410, 2007.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., Submit your next manuscript to BioMed Central and take full advantage of: ? Convenient online submission ? Thorough peer review ? No space constraints or color figure charges ? Immediate publication on acceptance ? Inclusion in PubMed, CAS, Scopus and Google Scholar ? Research which is freely available for redistribution, J Comput Chem, vol.25, issue.13, pp.1605-1617, 2004.