Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
A proposed mechanism for IS607-family serine transposases, Mobile DNA, vol.4, issue.1, p.24, 2013. ,
DOI : 10.1146/annurev.bi.58.070189.004405
Integrons, Annual Review of Genetics, vol.44, issue.1, pp.141-166, 2010. ,
DOI : 10.1146/annurev-genet-102209-163504
URL : https://hal.archives-ouvertes.fr/hal-00535771
Partial Chromosome Sequence of Spiroplasma citri Reveals Extensive Viral Invasion and Important Gene Decay, Applied and Environmental Microbiology, vol.76, issue.11, pp.3420-3426, 2010. ,
DOI : 10.1128/AEM.02954-09
Prophages and bacterial genomics: what have we learned so far?, Molecular Microbiology, vol.141, issue.Suppl. 1, pp.277-300, 2003. ,
DOI : 10.1046/j.1365-2958.2003.03580.x
Breaking and joining single-stranded DNA: the HUH endonuclease superfamily, Nature Reviews Microbiology, vol.36, issue.8, pp.525-538, 2013. ,
DOI : 10.1038/nrmicro3067
URL : https://hal.archives-ouvertes.fr/hal-00944976
Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis, Genome Research, vol.12, issue.7, pp.1075-1079, 2002. ,
DOI : 10.1101/gr.132102
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186626
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
URL : http://doi.org/10.1093/nar/gkh340
DNA Transposons and the Evolution of Eukaryotic Genomes, Annual Review of Genetics, vol.41, issue.1, pp.331-368, 2007. ,
DOI : 10.1146/annurev.genet.40.110405.090448
A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2, Nucleic Acids Research, vol.42, issue.6, pp.3707-3719, 2014. ,
DOI : 10.1093/nar/gkt1385
URL : https://hal.archives-ouvertes.fr/hal-01332620
Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi, Microbiology, vol.149, issue.11, pp.3099-3109, 2003. ,
DOI : 10.1099/mic.0.26529-0
A New Group of Tyrosine Recombinase-Encoding Retrotransposons, Molecular Biology and Evolution, vol.21, issue.4, pp.746-759, 2004. ,
DOI : 10.1093/molbev/msh072
Mechanisms of Site-Specific Recombination, Annual Review of Biochemistry, vol.75, issue.1, pp.567-605, 2006. ,
DOI : 10.1146/annurev.biochem.73.011303.073908
CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease, Mobile DNA, vol.5, issue.1, p.23, 2014. ,
DOI : 10.1186/1759-8753-5-23
is a DNA integrase that generates target site duplications, Nucleic Acids Research, vol.43, issue.22, pp.10576-10587 ,
DOI : 10.1093/nar/gkv1180
Mechanisms of DNA transposition. Microbiol Spectr, pp.3-0034, 2015. ,
The struggle for life of the genome's selfish architects, Biology Direct, vol.6, issue.1, p.19, 2011. ,
DOI : 10.1534/genetics.105.051714
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria, Nucleic Acids Research, vol.20, issue.13, pp.3279-3285, 1992. ,
DOI : 10.1093/nar/20.13.3279
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members, Nucleic Acids Research, vol.33, issue.12, pp.3875-3896, 2005. ,
DOI : 10.1093/nar/gki702
Repetitive Sequences in Complex Genomes: Structure and Evolution, Annual Review of Genomics and Human Genetics, vol.8, issue.1, pp.241-259, 2007. ,
DOI : 10.1146/annurev.genom.8.080706.092416
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons Self-synthesizing DNA transposons in eukaryotes, PLoS Biol. Proc Natl Acad Sci, vol.3, issue.103, pp.1814540-4545, 2005. ,
A universal classification of eukaryotic transposable elements implemented in Repbase, Nature Reviews Genetics, vol.8, issue.5, pp.411-412, 2008. ,
DOI : 10.1038/nrg2165-c1
Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon, Biology Direct, vol.59, issue.3, p.20, 2015. ,
DOI : 10.1186/s13062-015-0055-8
Mobile Elements: Drivers of Genome Evolution, Science, vol.303, issue.5664, pp.1626-1632, 2004. ,
DOI : 10.1126/science.1089670
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
Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nature Reviews Genetics, vol.4, issue.3, pp.184-192 ,
DOI : 10.1038/nature13011
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
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses, Biology Direct, vol.9, issue.1, p.6, 2014. ,
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/pasteur-00994115
Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes, Annals of the New York Academy of Sciences, vol.9, issue.1, pp.41-53, 2015. ,
DOI : 10.1111/nyas.12675
URL : https://hal.archives-ouvertes.fr/hal-01436107
Insights into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids, PLoS ONE, vol.21, issue.2, p.49044, 2013. ,
DOI : 10.1371/journal.pone.0049044.s012
URL : https://hal.archives-ouvertes.fr/hal-00748527
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
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biology, vol.12, issue.1, p.36, 2014. ,
DOI : 10.1093/molbev/mst197
URL : https://hal.archives-ouvertes.fr/pasteur-01001796
Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1, Biochemical Society Transactions, vol.16, issue.1, pp.104-106, 2011. ,
DOI : 10.1073/pnas.0902910106
Annotation and Classification of CRISPR-Cas Systems, Methods Mol Biol, vol.1311, pp.47-75, 2015. ,
DOI : 10.1007/978-1-4939-2687-9_4
Evolution and classification of the CRISPR???Cas systems, Nature Reviews Microbiology, vol.35, issue.6, pp.467-477, 2011. ,
DOI : 10.1038/nrmicro2577
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes, Extremophiles, vol.6, issue.5, pp.877-893, 2014. ,
DOI : 10.1007/s00792-014-0672-7
An updated evolutionary classification of CRISPR???Cas systems, Nature Reviews Microbiology, vol.41, issue.11, pp.722-736, 2015. ,
DOI : 10.1038/nrmicro3569
CDD: conserved domains and protein three-dimensional structure, Nucleic Acids Research, vol.41, issue.D1, pp.348-352, 2013. ,
DOI : 10.1093/nar/gks1243
URL : http://doi.org/10.1093/nar/gks1243
Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, vol.155, pp.733-740, 2009. ,
Cas1???Cas2 complex formation mediates spacer acquisition during CRISPR???Cas adaptive immunity, Nature Structural & Molecular Biology, vol.25, issue.6, pp.528-534, 2014. ,
DOI : 10.1038/nsmb.2820
Integrase-mediated spacer acquisition during CRISPR???Cas adaptive immunity, Nature, vol.14, issue.7542, pp.193-198, 2015. ,
DOI : 10.1038/nature14237
Unipro UGENE: a unified bioinformatics toolkit, Bioinformatics, vol.28, issue.8, pp.1166-1167, 2012. ,
DOI : 10.1093/bioinformatics/bts091
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/28/8/1166
Tn7 elements: Engendering diversity from chromosomes to episomes, Plasmid, vol.61, issue.1, pp.1-14, 2009. ,
DOI : 10.1016/j.plasmid.2008.09.008
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614081
A survey of transposable element classification systems ??? A call for a fundamental update to meet the challenge of their diversity and complexity, Molecular Phylogenetics and Evolution, vol.86, pp.90-109, 2015. ,
DOI : 10.1016/j.ympev.2015.03.009
FastTree 2?approximately maximum-likelihood trees for large alignments Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses, PLoS One Gene, vol.5, issue.390, pp.3-17, 2007. ,
Comparative architecture of transposase and integrase complexes, Nature Structural Biology, vol.8, issue.4, pp.302-307, 2001. ,
DOI : 10.1038/86166
A modular master on the move: the Tn916 family of mobile genetic elements, Trends in Microbiology, vol.17, issue.6, pp.251-258, 2009. ,
DOI : 10.1016/j.tim.2009.03.002
Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition Protospacer recognition motifs: mixed identities and functional diversity, Elife RNA Biol, vol.4, issue.10, pp.8716891-899, 2013. ,
A Contiguous 66-kb Barley DNA Sequence Provides Evidence for Reversible Genome Expansion, Genome Research, vol.10, issue.7, pp.908-915, 2000. ,
DOI : 10.1101/gr.10.7.908
HHsenser: exhaustive transitive profile search using HMM-HMM comparison, Nucleic Acids Research, vol.34, issue.Web Server, pp.374-378, 2006. ,
DOI : 10.1093/nar/gkl195
URL : http://doi.org/10.1093/nar/gkl195
CRISPR ??? a widespread system that provides acquired resistance against phages in bacteria and archaea, Nature Reviews Microbiology, vol.7, issue.3, pp.181-186, 2008. ,
DOI : 10.1038/nrmicro1793
Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, issue.7, pp.1009-1010, 2011. ,
DOI : 10.1093/bioinformatics/btr039
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065679
Genome Assembly, Rearrangement, and Repeats, Chemical Reviews, vol.107, issue.8, pp.3391-3406, 2007. ,
DOI : 10.1021/cr0683008
The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes, Genome Dyn, vol.7, pp.68-91, 2012. ,
DOI : 10.1159/000337126
Unravelling the structural and mechanistic basis of CRISPR???Cas systems, Nature Reviews Microbiology, vol.41, issue.7, pp.479-492, 2014. ,
DOI : 10.1093/nar/gku120
Dynamics of transposable elements: towards a community ecology of the genome, Trends in Genetics, vol.25, issue.7, pp.317-323, 2009. ,
DOI : 10.1016/j.tig.2009.05.003
URL : https://hal.archives-ouvertes.fr/hal-00428403
A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, issue.12, pp.973-982, 2007. ,
DOI : 10.1038/nrg2165
URL : https://hal.archives-ouvertes.fr/hal-00169819
Comparative Genomic Analysis Reveals Multiple Long Terminal Repeats, Lineage-Specific Amplification, and Frequent Interelement Recombination for Cassandra Retrotransposon in Pear (Pyrus bretschneideri Rehd.), Genome Biology and Evolution, vol.6, issue.6, pp.1423-1436, 2014. ,
DOI : 10.1093/gbe/evu114
Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment, The ISME Journal, vol.47, issue.10, pp.2191-2205, 2015. ,
DOI : 10.5194/gmd-3-565-2010
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579472