The enigmatic archaeal virosphere, Nat Rev Microbiol, vol.15, pp.724-739, 2017. ,
DOI : 10.1038/nrmicro.2017.125
URL : https://hal.archives-ouvertes.fr/pasteur-01977353
40 Years of archaeal virology: expanding viral diversity, Virology, pp.369-378, 2015. ,
The double-stranded DNA virosphere as a modular hierarchical network of gene sharing, MBio, vol.7, pp.978-994, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977375
Viruses of archaea: Structural, functional, environmental and evolutionary genomics, Virus Res, vol.244, pp.181-193, 2018. ,
DOI : 10.1016/j.virusres.2017.11.025
URL : https://hal.archives-ouvertes.fr/pasteur-01977349
Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements, J Virol, vol.90, pp.11043-11055, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977374
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
Multiple consecutive initiation of replication producing novel brush-like intermediates at the termini of linear viral dsDNA genomes with hairpin ends, Nucleic Acids Res, vol.44, pp.8799-8809, 2016. ,
Unique genome replication mechanism of the archaeal virus AFV1, Mol Microbiol, vol.92, pp.1313-1325, 2014. ,
Identification, characterization, and application of the replicon region of the halophilic temperate sphaerolipovirus SNJ1, J Bacteriol, vol.198, pp.1952-1964, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977378
Protein-protein interactions leading to recruitment of the host DNA sliding clamp by the hyperthermophilic Sulfolobus islandicus rodshaped virus 2, J Virol, vol.88, pp.7105-7108, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977399
Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205, Virology, vol.434, pp.233-241, 2012. ,
Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae, Arch Virol, vol.159, pp.1541-1554, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977401
Archaeal Haloarcula californiae Icosahedral virus 1 highlights conserved elements in icosahedral membrane-containing DNA viruses from extreme environments, MBio, vol.7, pp.699-715, 2016. ,
SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake, Virology, vol.335, pp.22-33, 2005. ,
PH1: an archaeovirus of Haloarcula hispanica related to SH1 and HHIV-2, Archaea, vol.2013, pp.1-17, 2013. ,
Closely related archaeal Haloarcula hispanica icosahedral viruses HHIV-2 and SH1 have nonhomologous genes encoding host recognition functions, J Virol, vol.86, pp.4734-4742, 2012. ,
DOI : 10.1128/jvi.00860-12
URL : https://jvi.asm.org/content/86/11/6383.full.pdf
Induction and preliminary characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5, Can J Microbiol, vol.53, pp.1106-1110, 2007. ,
Breaking and joining single-stranded DNA: the HUH endonuclease superfamily, Nat Rev Microbiol, vol.11, pp.525-538, 2013. ,
DOI : 10.1038/nrmicro3067
URL : https://hal.archives-ouvertes.fr/hal-00944976
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Curr Opin Virol, vol.3, pp.578-586, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977403
Plasmid rolling-circle replication: highlights of two decades of research, Plasmid, vol.53, pp.126-136, 2005. ,
A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors, Proc Natl Acad Sci, vol.94, pp.2626-2631, 1997. ,
Genetic analysis of a novel plasmid pZMX101 from Halorubrum saccharovorum: determination of the minimal replicon and comparison with the related haloarchaeal plasmid pSCM201, FEMS Microbiol Lett, vol.270, pp.104-108, 2007. ,
Plasmids from Euryarchaeota, Microbiol Spectr, vol.2, pp.27-2014, 2014. ,
DOI : 10.1128/microbiolspec.plas-0027-2014
URL : https://hal.archives-ouvertes.fr/hal-01478643
Single-stranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus, Proc Natl Acad Sci, vol.83, pp.2541-2545, 1986. ,
Complete sequence and molecular characterization of pNB101, a rolling-circle replicating plasmid from the haloalkaliphilic archaeon Natronobacterium sp. strain AS7091, Extremophiles, vol.8, pp.91-98, 2004. ,
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria, Nucleic Acids Res, vol.20, pp.3279-3285, 1992. ,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997. ,
The enigma of prokaryotic life in deep hypersaline anoxic basins, Science, vol.307, pp.121-123, 2005. ,
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes, Extremophiles, vol.18, pp.877-893, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977394
Living side by side with a virus: characterization of two novel plasmids from Thermococcus prieurii, a host for the spindle-shaped virus TPV1, Appl Environ Microbiol, vol.79, pp.3822-3828, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00832107
Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes, Arch Virol, vol.161, pp.249-256, 2016. ,
Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile, J Bacteriol, vol.178, pp.3232-3237, 1996. ,
Analysis of the halobacterial plasmid pHK2 minimal replicon, Gene, vol.153, pp.117-121, 1995. ,
Related haloarchaeal pleomorphic viruses contain different genome types, Nucleic Acids Res, vol.40, pp.5523-5534, 2012. ,
Insertion sequences in prokaryotic genomes, Curr Opin Microbiol, vol.9, pp.526-531, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00119306
Distribution of IS91 family insertion sequences in bacterial genomes: evolutionary implications, FEMS Microbiol Ecol, vol.42, pp.303-313, 2002. ,
Single-stranded DNA intermediates in IS91 rolling-circle transposition, Mol Microbiol, vol.39, pp.494-502, 2001. ,
IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids, Nucleic Acids Res, vol.20, p.3521, 1992. ,
Mobile ISCR elements: structure, functions, and role in the emergence, increasing and spreading of blocks of bacterial genes of multiple antibiotic resistance, Mol Gen Mikrobiol Virusol, vol.4, pp.135-146, 2012. ,
ISCR elements: novel genecapturing systems of the 21st century?, Microbiol Mol Biol Rev, vol.70, pp.296-316, 2006. ,
The IS200/IS605 family and "Peel and Paste" single-strand transposition mechanism, Microbiol Spectr, vol.3, pp.3-0039, 2015. ,
DOI : 10.1093/nar/gkt014
URL : https://academic.oup.com/nar/article-pdf/41/5/3302/16946038/gkt014.pdf
Insertion sequence diversity in archaea, Microbiol Mol Biol Rev, vol.71, pp.121-157, 2007. ,
CLANS: a Java application for visualizing protein families based on pairwise similarity, Bioinformatics, vol.20, pp.3702-3704, 2004. ,
DOI : 10.1093/bioinformatics/bth444
URL : https://academic.oup.com/bioinformatics/article-pdf/20/18/3702/521864/bth444.pdf
Site-specific integration of adeno-associated virus involves partial duplication of the target locus, Proc Natl Acad Sci, vol.106, pp.7571-7576, 2009. ,
Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes, BMC Evol Biol, vol.11, p.276, 2011. ,
DOI : 10.1186/1471-2148-11-276
URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-11-276
Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes, Ann N Y Acad Sci, vol.1341, pp.41-53, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01436107
WebLogo: a sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004. ,
DOI : 10.1101/gr.849004
URL : http://genome.cshlp.org/content/14/6/1188.full.pdf
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Brief Bioinform, 2017. ,
DOI : 10.1093/bib/bbx108
URL : https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbx108/19706293/bbx108.pdf
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009. ,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
, Journal of General Virology, vol.99, pp.416-421, 2018.