Snapshot of 615 virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta 616 icosahedral phage 1, Proc Natl Acad Sci U S A, vol.109, pp.7079-7084, 2012. ,
Candidatus 618 Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile 619 genome, Front Microbiol, vol.9, p.28, 2018. ,
Structure unifies the viral universe, Rev Biochem, vol.621, pp.795-822, 2012. ,
Discovery of several novel, widespread, 623 and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes, ISME J, 2019. ,
A novel lipothrixvirus, SIFV, of 626 the extremely thermophilic crenarchaeon Sulfolobus, Virology, vol.267, pp.252-266, 2000. ,
Haloarchaeal virus morphotypes, Biochimie, vol.118, pp.628-333, 2015. ,
Haloviruses of archaea, bacteria, and eukaryotes, 2015. ,
, Curr Opin Microbiol, vol.25, pp.40-48
Global network of specific 632 virus-host interactions in hypersaline environments, Environ Microbiol, vol.14, pp.426-440, 2012. ,
Archaeal viruses 634 multiply: temporal screening in a solar saltern, Viruses, vol.7, pp.1902-1926, 2015. ,
, , p.636, 2018.
, Extremely halophilic pleomorphic archaeal virus HRPV9 extends the diversity of pleolipoviruses with 637 integrases, Res Microbiol, vol.169, pp.500-504
The unexplored 639 diversity of pleolipoviruses: the surprising case of two viruses with identical major structural modules, Genes, vol.640, p.131, 2018. ,
, ICTV Virus Taxonomy Profile: Pleolipoviridae. J Gen Virol, vol.642, pp.2916-2917, 2017.
, , p.644, 2005.
, Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica, J Virol, vol.645, pp.9097-9107
SPAdes: a new 647 genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, pp.455-477, 2012. ,
The minichromosome maintenance replicative helicase, Cold Spring Harb 649 Perspect Biol, vol.5, p.12807, 2013. ,
A rapid and sensitive method for the quantitation of microgram quantities of protein 651 utilizing the principle of protein-dye binding, Anal Biochem, vol.72, pp.248-254, 1976. ,
Functional 653 interactions of archaea, bacteria and viruses in a hypersaline endolithic community, Environ Microbiol, vol.18, pp.654-2064, 2016. ,
, , p.656
Genomic plasticity in prokaryotes: the case of the square haloarchaeon, ISME J, vol.657, pp.235-245, 2007. ,
Virus-659 mediated archaeal hecatomb in the deep seafloor, Sci Adv, vol.2, p.1600492, 2016. ,
Temperate phages 661 acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like 662 recombinases, PLoS Genet, vol.10, p.1004181, 2014. ,
High level of 664 intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake, Proc Natl Acad, p.665, 2013. ,
, , vol.110, pp.16939-16944
, , p.667, 2016.
, Haloarcula hispanica pleomorphic virus 3 preserves high infectivity in saturated salt, Virology, vol.499, pp.40-51
669 (2016b) Archaeal Haloarcula californiae icosahedral virus 1 highlights conserved elements in icosahedral 670 membrane-containing DNA viruses from extreme environments ,
672 (2017) HCIV-1 and other tailless icosahedral internal membrane-containing viruses of the family 673 Sphaerolipoviridae ,
Seasonal 675 dynamics of extremely halophilic microbial communities in three Argentinian salterns, FEMS Microbiol Ecol, vol.676, p.92, 2016. ,
, , 2009.
The PL6-family plasmids of Haloquadratum are virus-related, vol.9, p.1070, 2018. ,
Complete genome sequence of 681 the model halovirus phiH1 (phiH1), Genes, p.9, 2018. ,
Halobacterium 683 salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1, Genes, p.10, 2019. ,
Haloquadratum walsbyi: 685 limited diversity in a global pond, PLoS One, vol.6, p.20968, 2011. ,
Novel 16S rRNA gene sequences retrieved from highly saline brine 687 sediments of kebrit deep, red Sea, Arch Microbiol, vol.172, pp.213-218, 1999. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic 689 Acids Res, vol.32, pp.1792-1797, 2004. ,
Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, pp.2460-691, 2010. ,
The structure of a prokaryotic 693 viral envelope protein expands the landscape of membrane fusion proteins, Nat Commun, vol.10, p.846, 2019. ,
A plasmid from an Antarctic 695 haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells, Nat Microbiol, vol.696, pp.1446-1455, 2017. ,
PHYLIP (phylogeny inference package), version 3, 1993. ,
A simple method for the isolation and purification of total 699 lipides from animal tissues, J Biol Chem, vol.226, pp.497-509, 1957. ,
, Euryarchaeota. Microbiol Spectr, vol.701, pp.27-2014, 2014.
, , p.703
Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses, PLoS One, vol.704, p.33802, 2012. ,
Protein-protein interactions 706 leading to recruitment of the host DNA sliding clamp by the hyperthermophilic Sulfolobus islandicus rod-707 shaped virus 2, J Virol, vol.88, pp.7105-7108, 2014. ,
PhageTerm: a tool for fast and 709 accurate determination of phage termini and packaging mechanism using next-generation sequencing data, 2017. ,
, Sci Rep, vol.7, p.8292
Strategies of adaptation of microorganisms of the 712 three domains of life to high salt concentrations, FEMS Microbiol Rev, vol.42, pp.353-375, 2018. ,
TIGRFAMs: a 714 protein family resource for the functional identification of proteins, Nucleic Acids Res, vol.29, pp.41-43, 2001. ,
Prodigal: prokaryotic 716 gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, p.119, 2010. ,
The double-stranded DNA virosphere as a modular 718 hierarchical network of gene sharing, vol.7, pp.978-00916, 2016. ,
Bipartite network analysis of the archaeal 720 virosphere: evolutionary connections between viruses and capsidless mobile elements, J Virol, vol.90, pp.11043-721, 2016. ,
Haloarcula hispanica spec, p.723, 1986. ,
two new species of extremely halophilic archaebacteria, Syst Appl Microbiol, vol.724, pp.75-79 ,
Genomic sequences of 726 bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages, J Mol Biol, vol.727, pp.27-51, 2000. ,
Techniques of Lipidology: Isolation, Analysis and Identification of 729 Lipids, 1972. ,
The logic of DNA replication in double-stranded DNA 731 viruses: insights from global analysis of viral genomes, Nucleic Acids Res, vol.44, pp.4551-4564, 2016. ,
Local biotic environment shapes the 733 spatial scale of bacteriophage adaptation to bacteria, Am Nat, vol.177, pp.440-451, 2011. ,
Order to the viral universe, J Virol, vol.84, pp.12476-12479, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977412
Comparative analysis of the mosaic genomes of tailed 736 archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed 737 viruses of bacteria, J Mol Biol, vol.397, pp.144-160, 2010. ,
The evolutionary history of archaeal MCM 739 helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements, Mol Biol, vol.740, pp.2716-2732, 2010. ,
Genomics of bacterial and archaeal 742 viruses: dynamics within the prokaryotic virosphere, Microbiol Mol Biol Rev, vol.75, pp.610-635, 2011. ,
A thaumarchaeal provirus testifies 744 for an ancient association of tailed viruses with archaea, Biochem Soc Trans, vol.39, pp.82-88, 2011. ,
Viruses of archaea: 746 structural, functional, environmental and evolutionary genomics, Virus Res, vol.244, pp.181-193, 2018. ,
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-748 Based Phylogeny Inference Program, Mol Biol Evol, vol.32, pp.2798-2800, 2015. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01283927
, , 2013.
, Cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon Haloferax mediterranei, J Bacteriol, vol.195, pp.751-867
Identification and characterization 753 of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain, 2015. ,
, Mol Microbiol, vol.98, pp.1002-1020
Detection of novel recombinases 756 in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs, Nucleic Acids Res, vol.38, pp.3952-757, 2010. ,
Novel Caudovirales 759 associated with Marine Group I Thaumarchaeota assembled from metagenomes, Environ Microbiol, 2019. ,
tRNAscan-SE: a program for improved detection of transfer RNA genes in 762 genomic sequence, Nucleic Acids Res, vol.25, pp.955-964, 1997. ,
The adaptive immune system of Haloferax volcanii, Life (Basel), vol.764, pp.521-537, 2015. ,
Dark matter in 766 archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes, Extremophiles, vol.767, pp.877-893, 2014. ,
VICTOR: genome-based phylogeny and classification of prokaryotic 769 viruses, Bioinformatics, vol.33, pp.3396-3404, 2017. ,
Genome sequence-based species 771 delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, vol.14, p.60, 2013. ,
Expanding the marine virosphere using 773 metagenomics, PLoS Genet, vol.9, p.1003987, 2013. ,
HF1 and HF2: novel bacteriophages of halophilic archaea, Virology, vol.775, pp.678-684, 1993. ,
Diversity of Haloquadratum and other 777 haloarchaea in three, geographically distant, Australian saltern crystallizer ponds, Extremophiles, vol.14, pp.161-169, 2010. ,
Molecular ecology of extremely halophilic Archaea and Bacteria, FEMS Microbiol Ecol, vol.39, pp.1-779, 2002. ,
Occurrence of virus-like particles in the Dead Sea, Extremophiles, vol.781, pp.143-149, 1997. ,
Sequence analysis of an 783 Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China. BMC Genomics, vol.8, p.410, 2007. ,
The archaeal PCNA proteins, Biochem Soc Trans, vol.39, pp.20-24, 2011. ,
Origins of highly 786 mosaic mycobacteriophage genomes, Cell, vol.113, pp.171-182, 2003. ,
Novel abundant oceanic 788 viruses of uncultured Marine Group II Euryarchaeota, Curr Biol, vol.27, pp.1362-1368, 2017. ,
Modified coat protein forms the 790 flexible spindle-shaped virion of haloarchaeal virus His1, Environ Microbiol, vol.15, pp.1674-1686, 2013. ,
An ssDNA virus infecting archaea: 792 a new lineage of viruses with a membrane envelope, Mol Microbiol, vol.72, pp.307-319, 2009. ,
The single-stranded DNA genome 794 of novel archaeal virus halorubrum pleomorphic virus 1 is enclosed in the envelope decorated with 795 glycoprotein spikes, J Virol, vol.84, pp.788-798, 2010. ,
Archaeal viruses and 797 bacteriophages: comparisons and contrasts, Trends Microbiol, vol.22, pp.334-344, 2014. ,
Pleolipoviridae, a newly 799 proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA 800 genomes, Arch Virol, vol.161, pp.249-256, 2016. ,
, , p.802, 2012.
, Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea, J Virol, vol.86, pp.5067-803
Structure of 805 the archaeal head-tailed virus HSTV-1 completes the HK97 fold story, Proc Natl Acad Sci U S A, vol.110, pp.10604-806, 2013. ,
Insights into 808 head-tailed viruses infecting extremely halophilic archaea, J Virol, vol.87, pp.3248-3260, 2013. ,
Whole genome 810 comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity, Elife, vol.811, issue.4, p.6416, 2015. ,
The enigmatic 813 archaeal virosphere, Nat Rev Microbiol, vol.15, pp.724-739, 2017. ,
FastTree 2--approximately maximum-likelihood trees for large 815 alignments, PLoS One, vol.5, p.9490, 2010. ,
SINA: accurate high-throughput multiple sequence 817 alignment of ribosomal RNA genes, Bioinformatics, vol.28, pp.1823-1829, 2012. ,
FigTree 1.4.3 -a graphical viewer of phylogenetic trees and a program for producing 819 publication-ready figures, 2006. ,
Global phylogenomic analysis 821 disentangles the complex evolutionary history of DNA replication in archaea, Genome Biol Evol, vol.6, pp.192-212, 2014. ,
Viral and microbial 823 community dynamics in four aquatic environments, ISME J, vol.4, pp.739-751, 2010. ,
Inversion within the haloalkaliphilic virus phi Ch1 DNA 825 results in differential expression of structural proteins, Mol Microbiol, vol.52, pp.413-426, 2004. ,
VirSorter: mining viral signal from microbial 827 genomic data, PeerJ, vol.3, p.985, 2015. ,
Metavir 2: new tools for viral 829 metagenome comparison and assembled virome analysis, BMC Bioinformatics, vol.15, p.76, 2014. ,
Analysis of metagenomic 831 data reveals common features of halophilic viral communities across continents, Environ Microbiol, vol.18, pp.889-832, 2016. ,
Structural 834 basis for assembly of vertical single beta-barrel viruses, Nat Commun, vol.10, p.1184, 2019. ,
Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for 836 the separation of proteins in the range from 1 to 100 kDa, Anal Biochem, vol.166, pp.368-379, 1987. ,
Related haloarchaeal pleomorphic viruses 838 contain different genome types, Nucleic Acids Res, vol.40, pp.5523-5534, 2012. ,
Snapshot of 840 haloarchaeal tailed virus genomes, RNA Biol, vol.10, pp.803-816, 2013. ,
Diversity of virus-842 host systems in hypersaline Lake Retba, Senegal. Environ Microbiol, vol.13, pp.1956-1972, 2011. ,
Monitoring physiological changes 844 in haloarchaeal cell during virus release, Viruses, vol.8, p.59, 2016. ,
The HHpred interactive server for protein homology detection 846 and structure prediction, Nucleic Acids Res, vol.33, pp.244-248, 2005. ,
Haloviruses HF1 and HF2: evidence for a recent and large 848 recombination event, J Bacteriol, vol.186, pp.2810-2817, 2004. ,
The COG 850 database: an updated version includes eukaryotes, BMC Bioinformatics, vol.4, p.41, 2003. ,
Review of the biogeography of the genus 852, 1998. ,
, Artemia (Crustacea, Anostraca). Journal of Biogeography, vol.25, pp.213-226
Genomic variation 854 and biogeography of Antarctic haloarchaea, vol.6, p.113, 2018. ,
A novel family of tyrosine integrases encoded 856 by the temperate pleolipovirus SNJ2, Nucleic Acids Res, vol.46, pp.2521-2536, 2018. ,
Rolling-circle 858 replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases 859 of the IS91 family insertion sequences, J Gen Virol, vol.99, pp.416-421, 2018. ,
Phage-861 bacteria infection networks, Trends Microbiol, vol.21, pp.82-91, 2013. ,
Microbial diversity of hypersaline 863 environments: a metagenomic approach, Curr Opin Microbiol, vol.25, pp.80-87, 2015. ,
Bacteriophage 865 diversity in the North Sea, Appl Environ Microbiol, vol.64, pp.4128-4133, 1998. ,
Putative archaeal viruses 867 from the mesopelagic ocean, PeerJ, vol.5, p.3428, 2017. ,
Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan 870 hyperhalophilic Bacteroidetes, ISME J, vol.869, pp.424-437, 2018. ,
Local adaptation of bacteriophages to 872 their bacterial hosts in soil, Science, vol.325, p.833, 2009. ,
Rapid bacteriophage 874 sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification, Virology, vol.875, pp.734-744, 1970. ,
Vast diversity of prokaryotic 877 virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic 878 sequence analysis, Virol J, vol.15, p.67, 2018. ,
Temperate membrane-containing halophilic 880 archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205, Virology, vol.434, pp.233-241, 2012. ,
A completely 882 reimplemented MPI bioinformatics toolkit with a new HHpred server at its core, J Mol Biol, vol.430, pp.2237-2243, 2018. ,