D. Mazel, Integrons: agents of bacterial evolution, Nature Reviews Microbiology, vol.91, issue.8, pp.608-620, 2006.
DOI : 10.1038/nrmicro1462

S. R. Partridge, Analysis of antibiotic resistance regions in Gram-negative bacteria, FEMS Microbiology Reviews, vol.35, issue.5, pp.820-855, 2011.
DOI : 10.1111/j.1574-6976.2011.00277.x

M. R. Gillings, Integrons: Past, Present, and Future, Microbiology and Molecular Biology Reviews, vol.78, issue.2, pp.257-277, 2014.
DOI : 10.1128/MMBR.00056-13

J. A. Escudero, C. Loot, A. Nivina, and D. Mazel, The Integron: Adaptation On Demand, Microbiology Spectrum, vol.3, issue.2, pp.3-0019, 2015.
DOI : 10.1128/microbiolspec.MDNA3-0019-2014

URL : https://hal.archives-ouvertes.fr/pasteur-01423322

C. M. Collis and R. M. Hall, Expression of antibiotic resistance genes in the integrated cassettes of integrons, Antimicrobial Agents and Chemotherapy, vol.39, issue.1, pp.155-162, 1995.
DOI : 10.1128/AAC.39.1.155

M. J. Joss, J. E. Koenig, M. Labbate, M. F. Polz, M. R. Gillings et al., ACID: annotation of cassette and integron data, BMC Bioinformatics, vol.10, issue.1, p.118, 2009.
DOI : 10.1186/1471-2105-10-118

Y. Boucher, M. Labbate, J. E. Koenig, and H. W. Stokes, Integrons: mobilizable platforms that promote genetic diversity in bacteria, Trends in Microbiology, vol.15, issue.7, pp.301-309, 2007.
DOI : 10.1016/j.tim.2007.05.004

C. A. Michael and M. Labbate, Gene cassette transcription in a large integron-associated array, BMC Genetics, vol.11, issue.1, p.82, 2010.
DOI : 10.1186/1471-2156-11-82

G. D. Recchia, H. W. Stokes, and R. M. Hall, Characterisation of specific and secondary recombination sites recognised by the integron DNA integrase, Nucleic Acids Research, vol.22, issue.11, pp.2071-2078, 1994.
DOI : 10.1093/nar/22.11.2071

G. D. Recchia and R. M. Hall, Plasmid evolution by acquisition of mobile gene cassettes: plasmid pIE723 contains the aadB gene cassette precisely inserted at a secondary site in the IncQ plasmid RSF1010, Molecular Microbiology, vol.29, issue.1, pp.179-187, 1995.
DOI : 10.1007/BF00339581

R. M. Hall, D. E. Brookes, and H. W. Stokes, Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point, Molecular Microbiology, vol.9, issue.8, pp.1941-1959, 1991.
DOI : 10.1016/0378-1119(85)90120-9

S. E. Nunes-duby, H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy, Similarities and differences among 105 members of the Int family of site-specific recombinases, Nucleic Acids Research, vol.26, issue.2, pp.391-406, 1998.
DOI : 10.1093/nar/26.2.391

C. M. Collis, G. D. Recchia, M. J. Kim, H. W. Stokes, and R. M. Hall, Efficiency of Recombination Reactions Catalyzed by Class 1 Integron Integrase IntI1, Journal of Bacteriology, vol.183, issue.8, pp.2535-2542, 2001.
DOI : 10.1128/JB.183.8.2535-2542.2001

D. Macdonald, G. Demarre, M. Bouvier, D. Mazel, and D. N. Gopaul, Structural basis for broad DNA-specificity in integron recombination, Nature, vol.54, issue.7088, pp.1157-1162, 2006.
DOI : 10.1038/nature04643

URL : https://hal.archives-ouvertes.fr/pasteur-00140781

M. Bouvier, M. Ducos-galand, C. Loot, D. Bikard, and D. Mazel, Structural Features of Single-Stranded Integron Cassette attC Sites and Their Role in Strand Selection, PLoS Genetics, vol.155, issue.9, p.1000632, 2009.
DOI : 10.1371/journal.pgen.1000632.s002

C. Frumerie, M. Ducos-galand, D. N. Gopaul, and D. Mazel, The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity, Nucleic Acids Research, vol.38, issue.2, pp.559-569, 2010.
DOI : 10.1093/nar/gkp990

N. Messier and P. H. Roy, Integron Integrases Possess a Unique Additional Domain Necessary for Activity, Journal of Bacteriology, vol.183, issue.22, pp.6699-6706, 2001.
DOI : 10.1128/JB.183.22.6699-6706.2001

S. R. Partridge, G. Tsafnat, E. Coiera, and J. R. Iredell, Gene cassettes and cassette arrays in mobile resistance integrons, FEMS Microbiology Reviews, vol.33, issue.4, pp.757-784, 2009.
DOI : 10.1111/j.1574-6976.2009.00175.x

R. M. Hall and C. M. Collis, Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination, Molecular Microbiology, vol.18, issue.4, pp.593-600, 1995.
DOI : 10.1111/j.1365-2958.1995.tb02368.x

D. A. Rowe-magnus, A. M. Guerout, L. Biskri, P. Bouige, and D. Mazel, Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae, Genome Research, vol.13, issue.3, pp.428-442, 2003.
DOI : 10.1101/gr.617103

J. J. Diaz-mejia, C. F. Amabile-cuevas, I. Rosas, and V. Souza, An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins, Microbiology, vol.154, issue.1, pp.94-102, 2008.
DOI : 10.1099/mic.0.2007/008649-0

D. R. Nemergut, M. S. Robeson, R. F. Kysela, A. P. Martin, S. K. Schmidt et al., Insights and inferences about integron evolution from genomic data, BMC Genomics, vol.9, issue.1, p.261, 2008.
DOI : 10.1186/1471-2164-9-261

R. M. Hall, Integrons and gene cassettes: hotspots of diversity in bacterial genomes, Annals of the New York Academy of Sciences, vol.189, issue.1, pp.71-78, 2012.
DOI : 10.1111/j.1749-6632.2012.06588.x

M. Gillings, Y. Boucher, M. Labbate, A. Holmes, S. Krishnan et al., The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance, Journal of Bacteriology, vol.190, issue.14, pp.5095-5100, 2008.
DOI : 10.1128/JB.00152-08

D. Mazel, B. Dychinco, V. A. Webb, and J. Davies, A Distinctive Class of Integron in the Vibrio cholerae Genome, Science, vol.280, issue.5363, pp.605-608, 1998.
DOI : 10.1126/science.280.5363.605

D. A. Rowe-magnus, A. M. Guerout, P. Ploncard, B. Dychinco, J. Davies et al., The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons, Proceedings of the National Academy of Sciences, vol.98, issue.2, pp.652-657, 2001.
DOI : 10.1073/pnas.98.2.652

B. Hochhut, Y. Lotfi, D. Mazel, S. M. Faruque, R. Woodgate et al., Molecular Analysis of Antibiotic Resistance Gene Clusters in Vibrio cholerae O139 and O1 SXT Constins, Antimicrobial Agents and Chemotherapy, vol.45, issue.11, pp.2991-3000, 2001.
DOI : 10.1128/AAC.45.11.2991-3000.2001

M. Iwanaga, C. Toma, T. Miyazato, S. Insisiengmay, N. Nakasone et al., Antibiotic Resistance Conferred by a Class I Integron and SXT Constin in Vibrio cholerae O1 Strains Isolated in Laos, Antimicrobial Agents and Chemotherapy, vol.48, issue.7, pp.2364-2369, 2004.
DOI : 10.1128/AAC.48.7.2364-2369.2004

M. R. Gillings, M. P. Holley, H. W. Stokes, and A. J. Holmes, Integrons in Xanthomonas: A source of species genome diversity, Proceedings of the National Academy of Sciences, vol.102, issue.12, pp.4419-4424, 2005.
DOI : 10.1073/pnas.0406620102

A. J. Holmes, M. R. Gillings, B. S. Nield, B. C. Mabbutt, K. M. Nevalainen et al., The gene cassette metagenome is a basic resource for bacterial genome evolution, Environmental Microbiology, vol.3, issue.5, pp.383-394, 2003.
DOI : 10.1046/j.1365-2958.2001.02604.x

A. Moura, I. Henriques, R. Ribeiro, and A. Correia, Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant, Journal of Antimicrobial Chemotherapy, vol.60, issue.6, pp.1243-1250, 2007.
DOI : 10.1093/jac/dkm340

T. Stalder, O. Barraud, M. Casellas, C. Dagot, and M. C. Ploy, Integron Involvement in Environmental Spread of Antibiotic Resistance, Frontiers in Microbiology, vol.3, p.119, 2012.
DOI : 10.3389/fmicb.2012.00119

M. R. Gillings, W. H. Gaze, A. Pruden, K. Smalla, J. M. Tiedje et al., Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution, The ISME Journal, vol.14, issue.6, pp.1269-1279, 2015.
DOI : 10.1073/pnas.1222743110

G. Tsafnat, E. Coiera, S. R. Partridge, J. Schaeffer, and J. R. Iredell, Context-driven discovery of gene cassettes in mobile integrons using a computational grammar, BMC Bioinformatics, vol.10, issue.1, p.281, 2009.
DOI : 10.1186/1471-2105-10-281

S. R. Eddy and R. Durbin, RNA sequence analysis using covariance models, Nucleic Acids Research, vol.22, issue.11, pp.2079-2088, 1994.
DOI : 10.1093/nar/22.11.2079

E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, vol.29, issue.22, pp.2933-2935, 2013.
DOI : 10.1093/bioinformatics/btt509

B. Neron, H. Menager, C. Maufrais, N. Joly, J. Maupetit et al., Mobyle: a new full web bioinformatics framework, Bioinformatics, vol.25, issue.22, pp.3005-3011, 2009.
DOI : 10.1093/bioinformatics/btp493

URL : https://hal.archives-ouvertes.fr/hal-01287963

A. Moura, M. Soares, C. Pereira, N. Leitao, I. Henriques et al., INTEGRALL: a database and search engine for integrons, integrases and gene cassettes, Bioinformatics, vol.25, issue.8, pp.1096-1098, 2009.
DOI : 10.1093/bioinformatics/btp105

R. C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

K. Katoh and D. M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-780, 2013.
DOI : 10.1093/molbev/mst010

S. R. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

M. K. Gibson, K. J. Forsberg, and G. Dantas, Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology, The ISME Journal, vol.38, issue.1, pp.207-216, 2015.
DOI : 10.1038/ismej.2014.106

R. D. Finn, J. Tate, J. Mistry, P. C. Coggill, S. J. Sammut et al., The Pfam protein families database, Nucleic Acids Research, vol.36, issue.Database, pp.281-288, 2008.
DOI : 10.1093/nar/gkm960

URL : https://hal.archives-ouvertes.fr/hal-01294685

P. J. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox et al., Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, vol.25, issue.11, pp.1422-1423, 2009.
DOI : 10.1093/bioinformatics/btp163

D. Hyatt, G. L. Chen, P. F. Locascio, M. L. Land, F. W. Larimer et al., Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, issue.1, p.119, 2010.
DOI : 10.1186/1471-2105-11-119

L. Bissonnette and P. H. Roy, Characterization of In0 of Pseudomonas aeruginosa plasmid pVS1, an ancestor of integrons of multiresistance plasmids and transposons of gram-negative bacteria., Journal of Bacteriology, vol.174, issue.4, pp.1248-1257, 1992.
DOI : 10.1128/jb.174.4.1248-1257.1992

M. Kearse, R. Moir, A. Wilson, S. Stones-havas, M. Cheung et al., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012.
DOI : 10.1093/bioinformatics/bts199

R. C. 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. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010.
DOI : 10.1186/1471-2148-10-210

L. T. Nguyen, H. A. Schmidt, A. Von-haeseler, and B. Q. Minh, IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.32, issue.1, pp.268-274, 2015.
DOI : 10.1093/molbev/msu300

M. Touchon, J. Cury, E. Yoon, L. Krizova, G. C. Cerqueira et al., The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences, Genome Biology and Evolution, vol.6, issue.10, pp.2866-2882, 2014.
DOI : 10.1093/gbe/evu225

URL : https://hal.archives-ouvertes.fr/pasteur-01132634

S. F. Altschul, T. L. Madden, A. A. Schäffer, 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.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, p.116, 2011.
DOI : 10.1186/1471-2105-8-396

URL : https://hal.archives-ouvertes.fr/hal-00698365

B. M. Lee, Y. J. Park, D. S. Park, H. W. Kang, J. G. Kim et al., The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice, Nucleic Acids Research, vol.33, issue.2, pp.577-586, 2005.
DOI : 10.1093/nar/gki206

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, and M. Chandler, ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Research, vol.34, issue.90001, pp.32-36, 2006.
DOI : 10.1093/nar/gkj014

URL : https://hal.archives-ouvertes.fr/hal-00021179

M. Touchon and E. P. Rocha, Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Molecular Biology and Evolution, vol.24, issue.4, pp.969-981, 2007.
DOI : 10.1093/molbev/msm014

H. J. Brown, H. W. Stokes, and R. M. Hall, The integrons In0, In2, and In5 are defective transposon derivatives., Journal of Bacteriology, vol.178, issue.15, pp.4429-4437, 1996.
DOI : 10.1128/jb.178.15.4429-4437.1996

G. Cambray, A. M. Guerout, and D. Mazel, 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

H. Segal, V. Francia, M. Garcia-lobo, J. M. Elisha, and G. , Reconstruction of an active integron recombination site after integration of a gene cassette at a secondary site, Antimicrob. Agents Chemother, vol.43, pp.2538-2541, 1999.

F. J. Silva, A. Latorre, and A. Moya, Why are the genomes of endosymbiotic bacteria so stable?, Trends in Genetics, vol.19, issue.4, pp.176-180, 2003.
DOI : 10.1016/S0168-9525(03)00041-6

B. Canback, I. Tamas, and S. G. Andersson, A Phylogenomic Study of Endosymbiotic Bacteria, Molecular Biology and Evolution, vol.21, issue.6, pp.1110-1122, 2004.
DOI : 10.1093/molbev/msh122

J. P. Mccutcheon and N. A. Moran, Extreme genome reduction in symbiotic bacteria, Nature Reviews Microbiology, vol.186, pp.13-26, 2012.
DOI : 10.1038/nrmicro2670

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, issue.6784, pp.299-304, 2000.
DOI : 10.1038/35012500

O. X. Cordero and P. Hogeweg, The impact of long-distance horizontal gene transfer on prokaryotic genome size, Proceedings of the National Academy of Sciences, vol.106, issue.51, pp.21748-21753, 2009.
DOI : 10.1073/pnas.0907584106

D. A. Baltrus, Exploring the costs of horizontal gene transfer, Trends in Ecology & Evolution, vol.28, issue.8, pp.489-495, 2013.
DOI : 10.1016/j.tree.2013.04.002

P. Salah, M. Bisaglia, P. Aliprandi, M. Uzan, C. Sizun et al., Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis, Nucleic Acids Research, vol.37, issue.16, pp.5578-5588, 2009.
DOI : 10.1093/nar/gkp547

URL : https://hal.archives-ouvertes.fr/hal-00469655

P. Mazodier and J. Davies, Gene Transfer Between Distantly Related Bacteria, Annual Review of Genetics, vol.25, issue.1, pp.147-171, 1991.
DOI : 10.1146/annurev.ge.25.120191.001051

T. Kloesges, O. Popa, W. Martin, and T. Dagan, Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths, Molecular Biology and Evolution, vol.28, issue.2, pp.1057-1074, 2011.
DOI : 10.1093/molbev/msq297

S. Nandi, J. J. Maurer, C. Hofacre, and A. O. Summers, Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter, Proceedings of the National Academy of Sciences, vol.101, issue.18, pp.7118-7122, 2004.
DOI : 10.1073/pnas.0306466101

L. Roux, F. Zouine, M. Chakroun, N. Binesse, J. Saulnier et al., Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity, Environ. Microbiol, vol.11, 1959.

A. M. Gestal, E. F. Liew, and N. V. Coleman, Natural transformation with synthetic gene cassettes: new tools for integron research and biotechnology, Microbiology, vol.157, issue.12, pp.3349-3360, 2011.
DOI : 10.1099/mic.0.051623-0

G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner, WebLogo: A Sequence Logo Generator, Genome Research, vol.14, issue.6, pp.1188-1190, 2004.
DOI : 10.1101/gr.849004