A. Achard and R. Leclercq, Characterization of a Small Mobilizable Transposon, MTnSag1, in Streptococcus agalactiae, Journal of Bacteriology, vol.189, issue.11, pp.4328-4331, 2007.
DOI : 10.1128/JB.00213-07

V. Alva, S. Z. Nam, J. Soding, and A. N. Lupas, The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis, Nucleic Acids Research, vol.44, issue.W1, pp.410-415, 2016.
DOI : 10.1093/nar/gkw348

C. Ambroset, C. Coluzzi, G. Guedon, M. D. Devignes, V. Loux et al., New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration, Frontiers in Microbiology, vol.8, issue.31, 2016.
DOI : 10.1038/nrmicro2382

URL : https://hal.archives-ouvertes.fr/hal-01262284

J. M. Auchtung, N. Aleksanyan, A. Bulku, and M. B. Berkmen, Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis, Plasmid, vol.86, 2016.
DOI : 10.1016/j.plasmid.2016.07.001

G. Bachrach, S. K. Haake, A. Glick, R. Hazan, R. Naor et al., Characterization of the Novel Fusobacterium nucleatum Plasmid pKH9 and Evidence of an Addiction System, Applied and Environmental Microbiology, vol.70, issue.12, pp.6957-6962, 2004.
DOI : 10.1128/AEM.70.12.6957-6962.2004

X. Bellanger, C. Morel, F. Gonot, A. Puymege, B. Decaris et al., Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture, Molecular Microbiology, vol.21, issue.4, pp.912-925, 2011.
DOI : 10.1111/j.1574-6976.1998.tb00355.x

X. Bellanger, S. Payot, N. Leblond-bourget, and G. Guedon, Conjugative and mobilizable genomic islands in bacteria: evolution and diversity, FEMS Microbiology Reviews, vol.38, issue.4, pp.720-760, 2014.
DOI : 10.1111/1574-6976.12058

URL : https://hal.archives-ouvertes.fr/hal-01474898

J. Bjorland, M. S. Bratlie, and T. Steinum, The smr gene resides on a novel plasmid pSP187 identified in a Staphylococcus pasteuri isolate recovered from unpasteurized milk, Plasmid, vol.57, issue.2, 2007.
DOI : 10.1016/j.plasmid.2006.08.004

M. Brochet, E. Couve, P. Glaser, G. Guedon, and S. Payot, Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae, Journal of Bacteriology, vol.190, issue.20, pp.6913-6917, 2008.
DOI : 10.1128/JB.00824-08

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 : 10.1128/jb.175.9.2713-2719.1993

E. Cabezon, J. Ripoll-rozada, A. Pena, F. De-la-cruz, and I. Arechaga, Towards an integrated model of bacterial conjugation, FEMS Microbiology Reviews, vol.39, pp.81-95, 2015.
DOI : 10.1111/1574-6976.12085

N. Carraro, D. Poulin, and V. Burrus, Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner, PLOS Genetics, vol.39, issue.Web Server issue, 2015.
DOI : 10.1371/journal.pgen.1005298.s002

C. Darbari, V. Waksman, and G. , Structural Biology of Bacterial Type IV Secretion Systems, Annual Review of Biochemistry, vol.84, issue.1, pp.603-629, 2015.
DOI : 10.1146/annurev-biochem-062911-102821

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, 2010.
DOI : 10.1128/jb.178.14.4157-4165.1996

S. Ebisu, Y. Murahashi, H. Takagi, K. Kadowaki, K. Yamaguchi et al., Nucleotide sequence and replication properties of the Bacillus borstelensis cryptic plasmid pHT926, Appl. Environ. Microbiol, vol.61, pp.3154-3157, 1995.

M. V. Francia, A. Varsaki, M. P. Garcillan-barcia, A. Latorre, C. Drainas et al., A classification scheme for mobilization regions of bacterial plasmids, FEMS Microbiology Reviews, vol.28, issue.1, pp.79-100, 2004.
DOI : 10.1016/j.femsre.2003.09.001

M. P. Garcillan-barcia, M. V. Francia, D. Cruz, and F. , 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

M. J. Gibbs, V. V. Smeianov, J. L. Steele, P. Upcroft, and B. A. Efimov, Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes, Molecular Biology and Evolution, vol.23, issue.6, pp.1097-1100, 2006.
DOI : 10.1093/molbev/msj122

E. Giovanetti, A. Brenciani, E. Tiberi, A. Bacciaglia, and P. E. Varaldo, ICESp2905, the erm(TR)-tet(O) Element of Streptococcus pyogenes, Is Formed by Two Independent Integrative and Conjugative Elements, Antimicrobial Agents and Chemotherapy, vol.56, issue.1, pp.591-594, 1128.
DOI : 10.1128/AAC.05352-11

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-00511794

R. Guerillot, V. Da-cunha, E. Sauvage, C. Bouchier, and P. Glaser, Modular Evolution of TnGBSs, a New Family of Integrative and Conjugative Elements Associating Insertion Sequence Transposition, Plasmid Replication, and Conjugation for Their Spreading, Journal of Bacteriology, vol.195, issue.9, pp.10-01745, 1128.
DOI : 10.1128/JB.01745-12

J. Guglielmini, F. De-la-cruz, and E. P. Rocha, Evolution of Conjugation and Type IV Secretion Systems, Molecular Biology and Evolution, vol.30, issue.2, pp.315-331, 2013.
DOI : 10.1093/molbev/mss221

URL : https://hal.archives-ouvertes.fr/pasteur-01374951

J. Guglielmini, B. Neron, S. S. Abby, M. P. Garcillan-barcia, F. De-la-cruz et al., Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Research, vol.42, issue.9, pp.5715-5727, 2014.
DOI : 10.1093/nar/gku194

URL : https://hal.archives-ouvertes.fr/pasteur-01374962

J. Guglielmini, L. Quintais, M. P. Garcillan-barcia, F. De-la-cruz, and E. P. Rocha, The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, 2011.
DOI : 10.1371/journal.pgen.1002222.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00647077

A. Ilangovan, S. Connery, and G. Waksman, Structural biology of the Gram-negative bacterial conjugation systems, Trends in Microbiology, vol.23, issue.5, 2015.
DOI : 10.1016/j.tim.2015.02.012

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: An information aesthetic for comparative genomics, Genome Research, vol.19, issue.9, pp.1639-1645, 2009.
DOI : 10.1101/gr.092759.109

URL : http://genome.cshlp.org/content/19/9/1639.full.pdf

B. Kunkel, R. Losick, and P. Stragier, The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene., Genes & Development, vol.4, issue.4, pp.525-535, 1990.
DOI : 10.1101/gad.4.4.525

C. A. Lee, A. Babic, and A. D. Grossman, Autonomous plasmidlike replication of a conjugative transposon, Mol. Microbiol, vol.75, 2010.

C. A. Lee, J. Thomas, and A. D. Grossman, The Bacillus subtilis Conjugative Transposon ICEBs1 Mobilizes Plasmids Lacking Dedicated Mobilization Functions, Journal of Bacteriology, vol.194, issue.12, pp.3165-3172, 2012.
DOI : 10.1128/JB.00301-12

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370859

F. Lorenzo-diaz, C. Fernandez-lopez, P. E. Douarre, A. Baez-ortega, C. Flores et al., Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer, Open Biol, 2016.

F. Lorenzo-diaz, C. Fernandez-lopez, M. P. Garcillan-barcia, and M. Espinosa, Bringing them together: Plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective, Plasmid, vol.74, pp.15-31, 2014.
DOI : 10.1016/j.plasmid.2014.05.004

B. Mcdonnell, J. Mahony, H. Neve, L. Hanemaaijer, J. P. Noben et al., ABSTRACT, Applied and Environmental Microbiology, vol.82, issue.17, pp.5153-5165, 1128.
DOI : 10.1128/AEM.00835-16

R. Meyer, Replication and conjugative mobilization of broad hostrange IncQ plasmids, Plasmid, vol.62, 2009.
DOI : 10.1016/j.plasmid.2009.05.001

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752045

J. G. Naglich, R. E. Andrews, and . Jr, Tn916-dependent conjugal transfer of PC194 and PUB110 from Bacillus subtilis into Bacillus thuringiensis subsp. israelensis, Plasmid, vol.20, issue.2, pp.113-126, 1988.
DOI : 10.1016/0147-619X(88)90014-5

R. M. Pollet, J. D. Ingle, J. P. Hymes, T. C. Eakes, K. Y. Eto et al., ABSTRACT, Journal of Bacteriology, vol.198, issue.6, pp.888-897, 1128.
DOI : 10.1128/JB.00832-15

A. Puymege, S. Bertin, G. Guedon, and S. Payot, Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNALys CTT gene, Molecular Genetics and Genomics, vol.45, issue.suppl 4, pp.1727-1740, 2015.
DOI : 10.1146/annurev-genet-110410-132412

URL : https://hal.archives-ouvertes.fr/hal-01475226

L. Rabinovich, N. Sigal, I. Borovok, R. Nir-paz, and A. A. Herskovits, Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence, Cell, vol.150, issue.4, pp.792-802, 2012.
DOI : 10.1016/j.cell.2012.06.036

URL : http://doi.org/10.1016/j.cell.2012.06.036

J. P. Ramsay, J. T. Sullivan, G. S. Stuart, I. L. Lamont, C. W. And-ronson et al., Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS Phylogenomics and the dynamic genome evolution of the genus Streptococcus Characterization of plasmids from human infant Bifidobacterium strains: sequence analysis and construction of E. coli- Bifidobacterium shuttle vectors, Mol. Microbiol. Genome Biol. Evol. Plasmid, vol.62, issue.60, pp.723-734, 2006.

S. A. Showsh, R. E. Andrews, and . Jr, Analysis of the Requirement for a pUB110 mob Region during Tn916-Dependent Mobilization, Plasmid, vol.41, issue.3, pp.179-186, 1999.
DOI : 10.1006/plas.1999.1398

F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Molecular Systems Biology, vol.7, issue.1, p.75, 2011.
DOI : 10.1093/nar/gkn174

C. Smillie, M. P. Garcillan-barcia, M. V. Francia, E. P. Rocha, D. Cruz et al., 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

K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. F. Kumar et al., MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

M. Trotter, O. Mcauliffe, M. Callanan, R. Edwards, G. F. Fitzgerald et al., Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactis provides insight into its adaptable nature, Gene, vol.366, issue.1, pp.189-199, 2006.
DOI : 10.1016/j.gene.2005.09.022

K. E. Weaver, S. M. Kwong, N. Firth, and M. V. Francia, The replicons of Gram-positive bacteria: A family of broadly distributed but narrow host range plasmids, Plasmid, vol.61, issue.2, pp.94-109, 2009.
DOI : 10.1016/j.plasmid.2008.11.004