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

F. De-la-cruz and J. Davies, Horizontal gene transfer and the origin of species: lessons from bacteria, Trends in Microbiology, vol.8, issue.3, pp.128-133, 2000.
DOI : 10.1016/S0966-842X(00)01703-0

H. Tettelin, D. Riley, C. Cattuto, and D. Medini, Comparative genomics: the bacterial pan-genome, Current Opinion in Microbiology, vol.11, issue.5, pp.472-477, 2008.
DOI : 10.1016/j.mib.2008.09.006

M. Lorenz and W. Wackernagel, Bacterial gene transfer by natural genetic transformation in the environment, Microbiol Rev, vol.58, pp.563-602, 1994.

M. Brochet, C. Rusniok, E. Couve, S. Dramsi, and C. Poyart, Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae, Proceedings of the National Academy of Sciences, vol.105, issue.41, pp.15961-15966, 2008.
DOI : 10.1073/pnas.0803654105

URL : https://hal.archives-ouvertes.fr/hal-00352709

A. Norman, L. Hansen, and S. Sorensen, Conjugative plasmids: vessels of the communal gene pool, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.304, issue.5667, pp.2275-2289, 2009.
DOI : 10.1126/science.1093857

S. Halary, J. Leigh, B. Cheaib, P. Lopez, and E. Bapteste, Network analyses structure genetic diversity in independent genetic worlds, Proceedings of the National Academy of Sciences, vol.107, issue.1, pp.127-132, 2010.
DOI : 10.1073/pnas.0908978107

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

C. Amábile-cuevas and M. Chicurel, Bacterial plasmids and gene flux, Cell, vol.70, issue.2, pp.189-199, 1992.
DOI : 10.1016/0092-8674(92)90095-T

M. Sebaihia, B. Wren, P. Mullany, N. Fairweather, and N. Minton, The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome, Nature Genetics, vol.21, issue.7, pp.779-786, 2006.
DOI : 10.1038/ng1830

C. Thomas, Horizontal Gene Pool: Bacterial Plasmids and Gene Spread, Amsterdam: CRC, vol.444, 2000.
DOI : 10.4324/9780203304334

J. Van-der-meer and V. Sentchilo, Genomic islands and the evolution of catabolic pathways in bacteria, Current Opinion in Biotechnology, vol.14, issue.3, pp.248-254, 2003.
DOI : 10.1016/S0958-1669(03)00058-2

F. De-la-cruz, L. Frost, R. Meyer, and E. Zechner, Conjugative DNA metabolism in Gram-negative bacteria, FEMS Microbiology Reviews, vol.34, issue.1, pp.18-40, 2010.
DOI : 10.1111/j.1574-6976.2009.00195.x

C. Smillie, M. Garcillan-barcia, M. Francia, E. Rocha, and F. De-la-cruz, Mobility of Plasmids, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.434-452, 2010.
DOI : 10.1128/MMBR.00020-10

URL : https://hal.archives-ouvertes.fr/pasteur-01374958

D. Thompson, L. Melchers, K. Idler, R. Schilperoort, and P. Hooykaas, B operon, Nucleic Acids Research, vol.16, issue.10, pp.4621-4636, 1988.
DOI : 10.1093/nar/16.10.4621

T. Lawley, W. Klimke, M. Gubbins, and L. Frost, F factor conjugation is a true type IV secretion system, FEMS Microbiology Letters, vol.224, issue.1, pp.1-15, 2003.
DOI : 10.1016/S0378-1097(03)00430-0

G. Sampei, N. Furuya, K. Tachibana, Y. Saitou, and T. Suzuki, Complete genome sequence of the incompatibility group I1 plasmid R64, Plasmid, vol.64, issue.2, pp.92-103, 2010.
DOI : 10.1016/j.plasmid.2010.05.005

M. Juhas, D. Crook, I. Dimopoulou, G. Lunter, and R. Harding, Novel Type IV Secretion System Involved in Propagation of Genomic Islands, Journal of Bacteriology, vol.189, issue.3, pp.761-771, 2007.
DOI : 10.1128/JB.01327-06

V. Burrus, G. Pavlovic, B. Decaris, and G. Guedon, Conjugative transposons: the tip of the iceberg, Molecular Microbiology, vol.67, issue.3, pp.601-610, 2002.
DOI : 10.1046/j.1365-2958.2002.03191.x

R. Wozniak and M. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-563, 2010.
DOI : 10.1038/nrmicro2382

B. Hochhut and M. Waldor, Site-specific integration of the conjugal Vibrio cholerae SXT element into prfC, Molecular Microbiology, vol.178, issue.1, pp.99-110, 1999.
DOI : 10.1046/j.1365-2958.1997.3911758.x

R. Ravatn, S. Studer, A. Zehnder, and J. Van-der-meer, Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. Strain B13, J Bacteriol, vol.180, pp.5505-5514, 1998.

M. Caparon and J. Scott, Excision and insertion of the conjugative transposon Tn916 involves a novel recombination mechanism, Cell, vol.59, issue.6, pp.1027-1034, 1989.
DOI : 10.1016/0092-8674(89)90759-9

L. Rajeev, K. Malanowska, and J. Gardner, Challenging a Paradigm: the Role of DNA Homology in Tyrosine Recombinase Reactions, Microbiology and Molecular Biology Reviews, vol.73, issue.2, pp.300-309, 2009.
DOI : 10.1128/MMBR.00038-08

M. Brochet, D. Cunha, V. Couve, E. Rusniok, C. Trieu-cuot et al., Atypical association of DDE transposition with conjugation specifies a new family of mobile elements, Molecular Microbiology, vol.144, issue.4, pp.948-959, 2009.
DOI : 10.1111/j.1365-2958.2008.06579.x

H. Wang and P. Mullany, The Large Resolvase TndX Is Required and Sufficient for Integration and Excision of Derivatives of the Novel Conjugative Transposon Tn5397, Journal of Bacteriology, vol.182, issue.23, pp.6577-6583, 2000.
DOI : 10.1128/JB.182.23.6577-6583.2000

F. Chumley, R. Menzel, and J. Roth, Hfr formation directed by tn10, Genetics, vol.91, pp.639-655, 1979.

J. Casey, C. Daly, and G. Fitzgerald, Chromosomal integration of plasmid DNA by homologous recombination in Enterococcus faecalis and Lactococcus lactis subsp. lactis hosts harboring Tn919, Appl Environ Microbiol, vol.57, pp.2677-2682, 1991.

C. Lee, A. Babic, and A. Grossman, Autonomous plasmid-like replication of a conjugative transposon, Molecular Microbiology, vol.9, issue.2, pp.268-279, 2010.
DOI : 10.1111/j.1365-2958.2009.06985.x

B. Doublet, D. Boyd, M. Mulvey, and A. Cloeckaert, genomic island 1 is an integrative mobilizable element, Molecular Microbiology, vol.49, issue.6, pp.1911-1924, 2005.
DOI : 10.1111/j.1365-2958.2005.04520.x

G. Douard, K. Praud, A. Cloeckaert, and B. Doublet, The Salmonella Genomic Island 1 Is Specifically Mobilized In Trans by the IncA/C Multidrug Resistance Plasmid Family, PLoS ONE, vol.42, issue.12, 2010.
DOI : 10.1371/journal.pone.0015302.s001

A. Daccord, D. Ceccarelli, and V. Burrus, Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands, Molecular Microbiology, vol.5, issue.3, pp.576-588, 2010.
DOI : 10.1111/j.1365-2958.2010.07364.x

U. Antonenka, C. Nolting, J. Heesemann, and A. Rakin, Horizontal transfer of Yersinia high-pathogenicity island by the conjugative RP4 attB target-presenting shuttle plasmid, Molecular Microbiology, vol.30, issue.3, pp.727-734, 2005.
DOI : 10.1111/j.1365-2958.2005.04722.x

U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker, Genomic islands in pathogenic and environmental microorganisms, Nature Reviews Microbiology, vol.31, issue.5, pp.414-424, 2004.
DOI : 10.1006/plas.1997.1280

D. Hofreuter, S. Odenbreit, and R. Haas, Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system, Molecular Microbiology, vol.63, issue.2, pp.379-391, 2001.
DOI : 10.1046/j.1365-2958.2001.02502.x

M. Llosa, C. Roy, and C. Dehio, Bacterial type IV secretion systems in human disease, Molecular Microbiology, vol.70, issue.2, pp.141-151, 2009.
DOI : 10.1111/j.1365-2958.2009.06751.x

A. Frank, C. Alsmark, M. Thollesson, and S. Andersson, Functional Divergence and Horizontal Transfer of Type IV Secretion Systems, Molecular Biology and Evolution, vol.22, issue.5, pp.1325-1336, 2005.
DOI : 10.1093/molbev/msi124

M. Juhas, P. Power, R. Harding, D. Ferguson, and I. Dimopoulou, Sequence and functional analyses of Haemophilus spp. genomic islands, Genome Biology, vol.8, issue.11, p.237, 2007.
DOI : 10.1186/gb-2007-8-11-r237

R. Wozniak, D. Fouts, M. Spagnoletti, M. Colombo, and D. Ceccarelli, Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs, PLoS Genetics, vol.40, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000786.s002

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

V. Burrus and M. Waldor, Shaping bacterial genomes with integrative and conjugative elements, Research in Microbiology, vol.155, issue.5, pp.376-386, 2004.
DOI : 10.1016/j.resmic.2004.01.012

C. Smith and A. Parker, Identification of a circular intermediate in the transfer and transposition of Tn4555, a mobilizable transposon from Bacteroides spp., Journal of Bacteriology, vol.175, issue.9, pp.2682-2691, 1993.
DOI : 10.1128/jb.175.9.2682-2691.1993

N. Shoemaker, G. Wang, A. Stevens, and A. Salyers, Excision, transfer, and integration of NBU1, a mobilizable site-selective insertion element., Journal of Bacteriology, vol.175, issue.20, pp.6578-6587, 1993.
DOI : 10.1128/jb.175.20.6578-6587.1993

E. Grohmann, G. Muth, and M. Espinosa, Conjugative Plasmid Transfer in Gram-Positive Bacteria, Microbiology and Molecular Biology Reviews, vol.67, issue.2, pp.277-301, 2003.
DOI : 10.1128/MMBR.67.2.277-301.2003

J. Vogelmann, M. Ammelburg, C. Finger, J. Guezguez, and D. Linke, resembles bacterial chromosome segregation by FtsK/SpoIIIE, The EMBO Journal, vol.180, issue.11, pp.2246-2254, 2011.
DOI : 10.1038/emboj.2011.121

J. Vogel, H. Andrews, S. Wong, and R. Isberg, Conjugative Transfer by the Virulence System of Legionella pneumophila, Science, vol.279, issue.5352, pp.873-876, 1998.
DOI : 10.1126/science.279.5352.873

A. Seubert, R. Hiestand, F. De-la-cruz, and C. Dehio, A bacterial conjugation machinery recruited for pathogenesis, Molecular Microbiology, vol.277, issue.5, pp.1253-1266, 2003.
DOI : 10.1046/j.1365-2958.2003.03650.x

H. De-paz, F. Sangari, S. Bolland, J. Garcia-lobo, and C. Dehio, Functional interactions between type IV secretion systems involved in DNA transfer and virulence, Microbiology, vol.151, issue.11, pp.3505-3516, 2005.
DOI : 10.1099/mic.0.28410-0

G. Blanc, H. Ogata, C. Robert, S. Audic, and J. Claverie, Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome, Genome Research, vol.17, issue.11, pp.1657-1664, 2007.
DOI : 10.1101/gr.6742107

M. Marenda, V. Barbe, G. Gourgues, S. Mangenot, and E. Sagne, A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms, Journal of Bacteriology, vol.188, issue.11, pp.4137-4141, 2006.
DOI : 10.1128/JB.00114-06

L. Weinert, J. Welch, and F. J. , Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally, Proceedings of the Royal Society B: Biological Sciences, vol.7, issue.6, pp.3619-3627, 2009.
DOI : 10.1186/1741-7007-7-6

D. Prangishvili, S. Albers, I. Holz, H. Arnold, and K. Stedman, Conjugation in Archaea: Frequent Occurrence of Conjugative Plasmids inSulfolobus, Plasmid, vol.40, issue.3, pp.190-202, 1998.
DOI : 10.1006/plas.1998.1363

K. Stedman, Q. She, H. Phan, I. Holz, and H. Singh, pING Family of Conjugative Plasmids from the Extremely Thermophilic Archaeon Sulfolobus islandicus: Insights into Recombination and Conjugation in Crenarchaeota, Journal of Bacteriology, vol.182, issue.24, pp.7014-7020, 2000.
DOI : 10.1128/JB.182.24.7014-7020.2000

A. Salyers, N. Shoemaker, A. Stevens, and L. Li, Conjugative Transposons, Microbiol Rev, vol.59, pp.579-590, 1995.
DOI : 10.1007/978-1-4615-5925-2_5

C. Merlin, D. Springael, and A. Toussaint, Tn4371:A Modular Structure Encoding a Phage-like Integrase, aPseudomonas-like Catabolic Pathway, and RP4/Ti-like Transfer Functions, Plasmid, vol.41, issue.1, pp.40-54, 1999.
DOI : 10.1006/plas.1998.1375

J. Sullivan and C. Ronson, Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene, Proceedings of the National Academy of Sciences, vol.95, issue.9, pp.5145-5149, 1998.
DOI : 10.1073/pnas.95.9.5145

J. Klockgether, O. Reva, K. Larbig, and B. Tummler, Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C, Journal of Bacteriology, vol.186, issue.2, pp.518-534, 2004.
DOI : 10.1128/JB.186.2.518-534.2004

M. Gaillard, T. Vallaeys, F. Vorholter, M. Minoia, and C. Werlen, The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties, Journal of Bacteriology, vol.188, issue.5, pp.1999-2013, 2006.
DOI : 10.1128/JB.188.5.1999-2013.2006

N. Cho, H. Kim, J. Lee, S. Kim, and J. Kim, The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host cell interaction genes, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.7981-7986, 2007.
DOI : 10.1073/pnas.0611553104

J. Parkhill, M. Sebaihia, A. Preston, L. Murphy, and N. Thomson, Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica, Nature Genetics, vol.35, issue.1, pp.32-40, 2003.
DOI : 10.1038/ng1227

C. Alvarez-martinez and P. Christie, Biological Diversity of Prokaryotic Type IV Secretion Systems, Microbiology and Molecular Biology Reviews, vol.73, issue.4, pp.775-808, 2009.
DOI : 10.1128/MMBR.00023-09

P. Engel, W. Salzburger, M. Liesch, C. Chang, and S. Maruyama, Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella, PLoS Genetics, vol.52, issue.4, 2011.
DOI : 10.1371/journal.pgen.1001296.s011

W. Fischer, L. Windhager, S. Rohrer, M. Zeiller, and A. Karnholz, Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer, Nucleic Acids Research, vol.38, issue.18, pp.6089-6101, 2010.
DOI : 10.1093/nar/gkq378

B. Nystedt, A. Frank, M. Thollesson, and S. Andersson, Diversifying Selection and Concerted Evolution of a Type IV Secretion System in Bartonella, Molecular Biology and Evolution, vol.25, issue.2, pp.287-300, 2008.
DOI : 10.1093/molbev/msm252

D. Medini, A. Covacci, and C. Donati, Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems, PLoS Computational Biology, vol.340, issue.12, 2006.
DOI : 10.1371/journal.pcbi.0020173.st005

M. Naum, E. Brown, and R. Mason-gamer, Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens, Microbiology, vol.155, issue.10, pp.3187-3199, 2009.
DOI : 10.1099/mic.0.029892-0

M. Garcillan-barcia, M. Francia, and F. De-la-cruz, The diversity of conjugative relaxases and its application in plasmid classification, FEMS Microbiology Reviews, vol.33, issue.3, pp.657-687, 2009.
DOI : 10.1111/j.1574-6976.2009.00168.x

G. Preston, Metropolitan Microbes: Type III Secretion in Multihost Symbionts, Cell Host & Microbe, vol.2, issue.5, pp.291-294, 2007.
DOI : 10.1016/j.chom.2007.10.004

B. Lacroix, T. Tzfira, A. Vainstein, and V. Citovsky, A case of promiscuity: Agrobacterium's endless hunt for new partners, Trends in Genetics, vol.22, issue.1, pp.29-37, 2006.
DOI : 10.1016/j.tig.2005.10.004

J. Rocco and G. Churchward, The Integrase of the Conjugative Transposon Tn916 Directs Strand- and Sequence-Specific Cleavage of the Origin of Conjugal Transfer, oriT, by the Endonuclease Orf20, Journal of Bacteriology, vol.188, issue.6, pp.2207-2213, 2006.
DOI : 10.1128/JB.188.6.2207-2213.2006

J. Xu, M. Bjursell, J. Himrod, S. Deng, and L. Carmichael, A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis, Science, vol.299, issue.5615, pp.2074-2076, 2003.
DOI : 10.1126/science.1080029

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

M. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-552, 2006.
DOI : 10.1080/10635150600755453

URL : https://hal.archives-ouvertes.fr/lirmm-00136658

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446