M. Pietilä, T. Demina, N. Atanasova, H. Oksanen, and D. Bamford, Archaeal viruses and bacteriophages: comparisons and contrasts, Trends in Microbiology, vol.22, issue.6, pp.334-344, 2014.
DOI : 10.1016/j.tim.2014.02.007

D. Prangishvili, The Wonderful World of Archaeal Viruses, Annual Review of Microbiology, vol.67, issue.1, pp.565-585, 2013.
DOI : 10.1146/annurev-micro-092412-155633

D. Prangishvili, R. Garrett, and E. Koonin, Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life, Virus Research, vol.117, issue.1, pp.52-67, 2006.
DOI : 10.1016/j.virusres.2006.01.007

J. Snyder, B. Bolduc, and M. Young, 40 Years of archaeal virology: Expanding viral diversity, Virology, vol.479, issue.480, p.643, 2015.
DOI : 10.1016/j.virol.2015.03.031

D. Jacobs-sera, D. Russell, C. Ko, C. Bowman, N. Atanasova et al., Snapshot of haloarchaeal tailed virus 646 genomes, Virology RNA Biol, vol.479480, issue.10, pp.369-378803, 2013.

N. Atanasova, D. Bamford, and H. Oksanen, Virus-host interplay in high salt environments, Environmental Microbiology Reports, vol.434, issue.4, p.648, 2016.
DOI : 10.1111/1758-2229.12385

P. Pfister, A. Wasserfallen, R. Stettler, and T. Leisinger, Molecular analysis of Methanobacterium 650, 1998.

M. Krupovic, P. Forterre, and D. Bamford, Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria, Journal of Molecular Biology, vol.397, issue.1, pp.144-160, 2010.
DOI : 10.1016/j.jmb.2010.01.037

URL : https://hal.archives-ouvertes.fr/hal-00506375

A. Pawlowski, I. Rissanen, J. Bamford, M. Krupovic, and M. Jalasvuori, Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae, Archives of Virology, vol.434, issue.6, pp.1541-1554, 2014.
DOI : 10.1007/s00705-013-1970-6

N. Kalkkinen, J. Bamford, S. Tang, C. Chen, P. Chiang et al., Constituents of SH1, a novel lipid-containing virus infecting the 664 halophilic euryarchaeon Haloarcula hispanica, Smith M. 2013. PH1: an archaeovirus of 666, pp.9097-9107, 2005.

N. Abrescia, Insight into the assembly of viruses with vertical single beta-barrel major capsid 675 proteins, Structure, vol.23, issue.676, pp.1866-1877, 2015.

M. Krupovic and D. Bamford, Virus evolution: how far does the double ??-barrel viral lineage extend?, Nature Reviews Microbiology, vol.3, issue.12, pp.941-948, 2008.
DOI : 10.1128/JVI.79.14.9236-9243.2005

M. Krupovic and E. Koonin, Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nature Reviews Microbiology, vol.214, issue.2, pp.105-115, 2015.
DOI : 10.1186/1741-7007-12-36

M. Krupovic and D. Bamford, Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus 687, 2008.

M. Gaudin, M. Krupovic, E. Marguet, E. Gauliard, V. Cvirkaite-krupovic et al., Extracellular membrane vesicles harbouring viral genomes, Environmental Microbiology, vol.66, issue.4, pp.1167-690
DOI : 10.1111/1462-2920.12235

URL : https://hal.archives-ouvertes.fr/hal-01234212

D. Bernick, K. Karplus, L. Lui, J. Coker, J. Murphy et al., Complete 692, 2012.

M. Pietilä, E. Roine, A. Sencilo, D. Bamford, and H. Oksanen, Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes, Archives of Virology, vol.1831, issue.1, pp.249-256, 2016.
DOI : 10.1007/s00705-015-2613-x

X. Peng, T. Basta, M. Haring, R. Garrett, and D. Prangishvili, Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms, Virology, vol.364, issue.1, pp.237-243, 2007.
DOI : 10.1016/j.virol.2007.03.005

T. Mochizuki, M. Krupovic, G. Pehau-arnaudet, Y. Sako, P. Forterre et al., Archaeal 713 virus with exceptional virion architecture and the largest single-stranded DNA genome, Proc Natl, p.714, 2012.

M. Krupovic, E. Quemin, D. Bamford, P. Forterre, and D. Prangishvili, Unification of the Globally Distributed Spindle-Shaped Viruses of the Archaea, Journal of Virology, vol.88, issue.4, pp.2354-2358, 2014.
DOI : 10.1128/JVI.02941-13

URL : https://hal.archives-ouvertes.fr/hal-00951871

A. Gorlas, E. Koonin, N. Bienvenu, D. Prieur, and C. Geslin, TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus, Environmental Microbiology, vol.10, issue.2, pp.503-516, 2012.
DOI : 10.1111/j.1462-2920.2011.02662.x

URL : https://hal.archives-ouvertes.fr/hal-00775875

E. Iverson and K. Stedman, A genetic study of SSV1, the prototypical fusellovirus, Frontiers in Microbiology, vol.3, issue.724, p.36, 0200.
DOI : 10.3389/fmicb.2012.00200

P. Contursi, S. Fusco, R. Cannio, and Q. She, Molecular biology of fuselloviruses and their satellites, Extremophiles, vol.18, issue.4, p.731, 2014.
DOI : 10.1007/s00792-014-0634-0

M. Häring, G. Vestergaard, R. R. Chen, L. Garrett, R. Prangishvili et al., Virology: Independent virus development outside a host, Nature, vol.436, issue.7054, pp.1101-1102, 2005.
DOI : 10.1038/4361101a

R. Garrett, D. Prangishvili, S. Shah, M. Reuter, K. Stetter et al., Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles, Environmental Microbiology, vol.190, issue.11, pp.2918-2930, 2010.
DOI : 10.1111/j.1462-2920.2010.02266.x

Y. She, Q. Garrett, R. Huang, L. Lin, and L. , A novel single-tailed fusiform Sulfolobus virus STSV2 739 infecting model Sulfolobus species, Extremophiles, vol.18, issue.740, pp.51-60, 2014.

X. Xiang, L. Chen, X. Huang, Y. Luo, Q. She et al., Sulfolobus tengchongensis Spindle-Shaped Virus STSV1: Virus-Host Interactions and Genomic Features, Journal of Virology, vol.79, issue.14, pp.8677-8686, 2005.
DOI : 10.1128/JVI.79.14.8677-8686.2005

B. Bolduc, D. Shaughnessy, Y. Wolf, E. Koonin, F. Roberto et al., Identification of novel 748 positive-strand RNA viruses by metagenomic analysis of archaea, 2012.

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1659, 2006.
DOI : 10.1093/bioinformatics/btl158

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.3389-758, 1997.
DOI : 10.1093/nar/25.17.3389

M. Rosvall and C. Bergstrom, Maps of random walks on complex networks reveal community structure, Proceedings of the National Academy of Sciences, vol.105, issue.4, pp.1118-1123, 2008.
DOI : 10.1073/pnas.0706851105

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. Meier and J. Söding, Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling, PLOS Computational Biology, vol.10, issue.Suppl 1, pp.1004343-768, 2015.
DOI : 10.1371/journal.pcbi.1004343.s002

J. Söding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-769, 2005.
DOI : 10.1093/bioinformatics/bti125

M. Barber, Modularity and community detection in bipartite networks, Physical Review E, vol.76, issue.6, 2007.
DOI : 10.1103/PhysRevE.76.066102

J. Bascompte, P. Jordano, C. Melian, and J. Olesen, The nested assembly of plant-animal 778, 2003.

M. Krupovic and E. Koonin, Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Current Opinion in Microbiology, vol.31, issue.781, pp.25-33, 2016.
DOI : 10.1016/j.mib.2016.01.006

P. Béguin, N. Charpin, E. Koonin, P. Forterre, and M. Krupovic, Casposon integration shows strong 782 target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic, vol.783, 2016.

A. Hickman and F. Dyda, is a DNA integrase that generates target site duplications, Nucleic Acids Research, vol.43, issue.22, pp.10576-10587, 2015.
DOI : 10.1093/nar/gkv1180

C. Bath, T. Cukalac, K. Porter, and M. Smith, His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus, Virology, vol.350, issue.1, pp.228-239, 2006.
DOI : 10.1016/j.virol.2006.02.005

Y. Wang, L. Sima, J. Lv, S. Huang, Y. Liu et al., ABSTRACT, Journal of Bacteriology, vol.198, issue.14, pp.1952-1964, 2016.
DOI : 10.1128/JB.00131-16

URL : https://hal.archives-ouvertes.fr/hal-00953003

T. Mochizuki, Y. Sako, and D. Prangishvili, Provirus Induction in Hyperthermophilic Archaea: Characterization of Aeropyrum pernix Spindle-Shaped Virus 1 and Aeropyrum pernix Ovoid Virus 1, Journal of Bacteriology, vol.193, issue.19, p.793, 2011.
DOI : 10.1128/JB.05101-11

M. Krupovic and D. Bamford, Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly, Current Opinion in Virology, vol.1, issue.2, pp.118-124, 2011.
DOI : 10.1016/j.coviro.2011.06.001

M. Pietilä, P. Laurinmaki, D. Russell, C. Ko, D. Jacobs-sera et al., Casposons: a new 800, 2014.

M. Krupovic, M. Gonnet, W. Hania, P. Forterre, and G. Erauso, Insights into dynamics of mobile 803 genetic elements in hyperthermophilic environments from five new Thermococcus plasmids, PLoS, vol.804, 2013.

H. Arnold, Q. She, H. Phan, K. Stedman, D. Prangishvili et al., The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a 807 hybrid between a plasmid and a virus, Mol Microbiol, vol.806, issue.808, pp.217-226, 1999.

P. Lopez-garcia, P. Forterre, J. Van-der-oost, and G. Erauso, Plasmid pGS5 from the 812 hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled, J Bacteriol, vol.813, issue.814, pp.4998-5000, 2000.

A. Gorlas, M. Krupovic, P. Forterre, and C. Geslin, Living Side by Side with a Virus: Characterization of Two Novel Plasmids from Thermococcus prieurii, a Host for the Spindle-Shaped Virus TPV1, Applied and Environmental Microbiology, vol.79, issue.12, 2013.
DOI : 10.1128/AEM.00525-13

URL : https://hal.archives-ouvertes.fr/hal-00832107

T. Ilyina and E. Koonin, Conserved sequence motifs in the initiator proteins for rolling circle 74, 1992.

E. Koonin and V. Dolja, Virus world as an evolutionary network of viruses and capsidless selfish 75, 2014.

E. Koonin, T. Senkevich, and V. Dolja, The ancient Virus World and evolution of cells, Biol, vol.823, 2006.

E. Koonin, V. Dolja, and M. Krupovic, Origins and evolution of viruses of eukaryotes: The ultimate modularity, Virology, vol.479, issue.480, pp.2-25, 2015.
DOI : 10.1016/j.virol.2015.02.039

M. Krupovic, Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Current Opinion in Virology, vol.3, issue.5, pp.578-586, 2013.
DOI : 10.1016/j.coviro.2013.06.010

M. Krupovic, S. Gribaldo, D. Bamford, and P. Forterre, The evolutionary history of archaeal MCM 831 helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements, p.832, 2010.

D. Kazlauskas, M. Krupovic, and C. Venclovas, The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes, Nucleic Acids Research, vol.44, issue.10, pp.4551-4564, 2016.
DOI : 10.1093/nar/gkw322

M. Krupovic, V. Cvirkaite-krupovic, D. Prangishvili, and E. Koonin, Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease, Biology Direct, vol.25, issue.13, pp.65-82, 2015.
DOI : 10.1186/s13062-015-0093-2