S. Abedon and R. Calendar, The bacteriophages, 2005.

S. Abedon and J. Lejeune, Why bacteriophage encode exotoxins and other virulence factors, Evol Bioinform Online, vol.1, pp.97-110, 2005.

H. Ackermann, Salmonella Phages Examined in the Electron Microscope, Methods Mol Biol, vol.394, pp.213-234, 2007.
DOI : 10.1007/978-1-59745-512-1_11

G. Allison, A. D. Tran-dinh, N. Verma, and N. , Complete Genomic Sequence of SfV, a Serotype-Converting Temperate Bacteriophage of Shigellaflexneri, Journal of Bacteriology, vol.184, issue.7, pp.1974-1987, 2002.
DOI : 10.1128/JB.184.7.1974-1987.2002

S. Altschul, T. Madden, A. Schaffer, 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

F. Angly, B. Felts, and M. Breitbart, The Marine Viromes of Four Oceanic Regions, PLoS Biology, vol.8, issue.11, p.368, 2006.
DOI : 10.1371/journal.pbio.0040368.sd001

M. Asadulghani, Y. Ogura, T. Ooka, T. Itoh, A. Sawaguchi et al., The Defective Prophage Pool of Escherichia coli O157: Prophage???Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants, PLoS Pathogens, vol.97, issue.5, p.1000408, 2009.
DOI : 10.1371/journal.ppat.1000408.s013

T. Baba, A. T. Hasegawa, M. Takai, Y. Okumura, Y. Baba et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1038/msb4100050

R. Balbontin, N. Figueroa-bossi, J. Casadesus, and L. Bossi, Insertion Hot Spot for Horizontally Acquired DNA within a Bidirectional Small-RNA Locus in Salmonella enterica, Journal of Bacteriology, vol.190, issue.11, pp.4075-4078, 2008.
DOI : 10.1128/JB.00220-08

D. Banks, S. Beres, and J. Musser, The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence, Trends in Microbiology, vol.10, issue.11, pp.515-521, 2002.
DOI : 10.1016/S0966-842X(02)02461-7

S. Bigot, O. Saleh, C. Lesterlin, C. Pages, E. Karoui et al., KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase, The EMBO Journal, vol.19, issue.21, pp.3770-3780, 2005.
DOI : 10.1046/j.1365-2958.2003.03574.x
URL : https://hal.archives-ouvertes.fr/hal-00013989

G. Blum, M. Ott, A. Lischewski, A. Ritter, H. Imrich et al., Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen, Infect Immun, vol.62, pp.606-614, 1994.

L. Bossi, J. Fuentes, G. Mora, and N. Figueroa-bossi, Prophage Contribution to Bacterial Population Dynamics, Journal of Bacteriology, vol.185, issue.21, pp.6467-6471, 2003.
DOI : 10.1128/JB.185.21.6467-6471.2003

D. Botstein, A THEORY OF MODULAR EVOLUTION FOR BACTERIOPHAGES, Annals of the New York Academy of Sciences, vol.17, issue.1 Genetic Varia, pp.484-490, 1980.
DOI : 10.1016/S0022-2836(75)80127-6

E. Boyd and H. Brussow, Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved, Trends in Microbiology, vol.10, issue.11, pp.521-529, 2002.
DOI : 10.1016/S0966-842X(02)02459-9

M. Breitbart, M. Haynes, and S. Kelley, Viral diversity and dynamics in an infant gut, Research in Microbiology, vol.159, issue.5, pp.367-373, 2008.
DOI : 10.1016/j.resmic.2008.04.006

S. Brown, L. Chat, L. , D. Paepe, M. Taddei et al., Ecology of Microbial Invasions: Amplification Allows Virus Carriers to Invade More Rapidly When Rare, Current Biology, vol.16, issue.20, pp.2048-2052, 2006.
DOI : 10.1016/j.cub.2006.08.089

H. Brussow, C. Canchaya, and W. Hardt, Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion, Microbiology and Molecular Biology Reviews, vol.68, issue.3, pp.560-602, 2004.
DOI : 10.1128/MMBR.68.3.560-602.2004

A. Bukhari and M. Metlay, Genetic mapping of prophage Mu, Virology, vol.54, issue.1, pp.109-116, 1973.
DOI : 10.1016/0042-6822(73)90120-7

A. Campbell, Prophage insertion sites, Research in Microbiology, vol.154, issue.4, pp.277-282, 2003.
DOI : 10.1016/S0923-2508(03)00071-8

A. Campbell, D. Botstein, R. Hendrix, J. Roberts, F. Stahl et al., Evolution of the lambdoid phages, Lambda II. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory, pp.365-380, 1983.

A. Campbell, Chromosomal insertion sites for phages and plasmids., Journal of Bacteriology, vol.174, issue.23, pp.7495-7499, 1992.
DOI : 10.1128/jb.174.23.7495-7499.1992

A. Campbell, Preferential Orientation Preferential Orientation of Natural Lambdoid Prophages and Bacterial Chromosome Organization, Theoretical Population Biology, vol.61, issue.4, pp.503-507, 2002.
DOI : 10.1006/tpbi.2002.1604

C. Canchaya, G. Fournous, and H. Brussow, The impact of prophages on bacterial chromosomes, Molecular Microbiology, vol.413, issue.1, pp.9-18, 2004.
DOI : 10.1111/j.1365-2958.2004.04113.x

C. Canchaya, C. Proux, G. Fournoux, A. Bruttin, and H. Brussow, Prophage Genomics, Microbiology and Molecular Biology Reviews, vol.67, issue.2, pp.238-276, 2003.
DOI : 10.1128/MMBR.67.2.238-276.2003

S. Casjens, 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

E. Couturier and E. Rocha, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Molecular Microbiology, vol.52, issue.5, pp.1506-1518, 2006.
DOI : 10.1111/j.1365-2958.2006.05046.x

K. Creuzburg, S. Heeren, C. Lis, M. Kranz, M. Hensel et al., Genetic Background and Mobility of Variants of the Gene nleA in Attaching and Effacing Escherichia coli, Applied and Environmental Microbiology, vol.77, issue.24, pp.8705-8713, 2011.
DOI : 10.1128/AEM.06492-11

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

T. Cui, N. Moro-oka, K. Ohsumi, K. Kodama, T. Ohshima et al., Escherichia coli with a linear genome, EMBO reports, vol.183, issue.2, pp.181-187, 2007.
DOI : 10.1038/sj.embor.7400880

A. Dearborn, P. Laurinmaki, P. Chandramouli, C. Rodenburg, S. Wang et al., Structure and size determination of bacteriophage P2 and P4 procapsids: Function of size responsiveness mutations, Journal of Structural Biology, vol.178, issue.3, pp.215-224, 2012.
DOI : 10.1016/j.jsb.2012.04.002

U. Dobrindt, G. Blum-oehler, G. Nagy, G. Schneider, J. A. Gottschalk et al., Genetic Structure and Distribution of Four Pathogenicity Islands (PAI I536 to PAI IV536) of Uropathogenic Escherichia coli Strain 536, Infection and Immunity, vol.70, issue.11, pp.6365-6372, 2002.
DOI : 10.1128/IAI.70.11.6365-6372.2002

H. Dong, L. Nilsson, and C. Kurland, Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates, Journal of Molecular Biology, vol.260, issue.5, pp.649-663, 1996.
DOI : 10.1006/jmbi.1996.0428

I. Duggin and S. Bell, Termination Structures in the Escherichia coli Chromosome Replication Fork Trap, Journal of Molecular Biology, vol.387, issue.3, pp.532-539, 2009.
DOI : 10.1016/j.jmb.2009.02.027

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

R. Edgar, A. Rokney, M. Feeney, S. Semsey, M. Kessel et al., Bacteriophage infection is targeted to cellular poles, Molecular Microbiology, vol.124, issue.5, pp.1107-1116, 2008.
DOI : 10.1073/pnas.83.23.8934

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

G. Edlin, L. Lin, and R. Bitner, Reproductive fitness of P1, P2, and Mu lysogens of Escherichia coli, J Virol, vol.21, pp.560-564, 1977.

R. Edwards and F. Rohwer, Opinion: Viral metagenomics, Nature Reviews Microbiology, vol.51, issue.6, pp.504-510, 2005.
DOI : 10.1073/pnas.93.12.5854

E. Esnault, M. Valens, O. Espeli, and F. Boccard, Chromosome Structuring Limits Genome Plasticity in Escherichia coli, PLoS Genetics, vol.334, issue.12, p.226, 2007.
DOI : 10.1371/journal.pgen.0030226.st001

D. Fouts, Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Research, vol.34, issue.20, pp.5839-5851, 2006.
DOI : 10.1093/nar/gkl732

C. Garcia-aljaro, M. Muniesa, J. Jofre, and A. Blanch, Genotypic and Phenotypic Diversity among Induced, stx2-Carrying Bacteriophages from Environmental Escherichia coli Strains, Applied and Environmental Microbiology, vol.75, issue.2, pp.329-336, 2009.
DOI : 10.1128/AEM.01367-08

N. Garcia-russell, T. Harmon, T. Le, N. Amaladas, R. Mathewson et al., Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage 749, 2004.

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808
URL : https://hal.archives-ouvertes.fr/lirmm-00730410

G. Greub, J. Mege, and D. Raoult, Parachlamydia acanthamoebae Enters and Multiplies within Human Macrophages and Induces Their Apoptosis, Infection and Immunity, vol.72, issue.1, pp.5979-5985, 2003.
DOI : 10.1128/IAI.72.1.621.2004

A. Gruber, R. Lorenz, S. Bernhart, R. Neubock, and I. Hofacker, The Vienna RNA Websuite, Nucleic Acids Research, vol.36, issue.Web Server, pp.70-74, 2008.
DOI : 10.1093/nar/gkn188

R. Guerrero-ferreira, P. Viollier, B. Ely, J. Poindexter, M. Georgieva et al., Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus, Proceedings of the National Academy of Sciences, vol.108, issue.24, pp.9963-9968, 2011.
DOI : 10.1073/pnas.1012388108

H. Hendrickson and J. Lawrence, Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites, Molecular Microbiology, vol.59, issue.Pt 1, pp.42-56, 2007.
DOI : 10.1111/j.1365-2958.2007.05596.x

R. Hendrix, M. Smith, R. Burns, M. Ford, and G. Hatfull, Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage, Proceedings of the National Academy of Sciences, vol.96, issue.5, pp.2192-2197, 1999.
DOI : 10.1073/pnas.96.5.2192

A. Hermans, A. Beuling, A. Van-hoek, H. Aarts, T. Abee et al., Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates, Microbiology, vol.152, issue.7, pp.2137-2147, 2006.
DOI : 10.1099/mic.0.28850-0

H. Huang, H. Chang, C. Chou, C. Tseng, S. Ho et al., sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes, Nucleic Acids Research, vol.37, issue.Database, pp.150-154, 2009.
DOI : 10.1093/nar/gkn852

K. Huber and M. Waldor, Filamentous phage integration requires the host recombinases XerC and XerD, Nature, vol.63, issue.6889, pp.656-659, 2002.
DOI : 10.1006/plas.1996.0001

M. Itaya, K. Tsuge, M. Koizumi, and K. Fujita, From The Cover: Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome, Proceedings of the National Academy of Sciences, vol.102, issue.44, pp.15971-15976, 2005.
DOI : 10.1073/pnas.0503868102

G. Jobb, A. Von-haeseler, and K. Strimmer, TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics, BMC Evolutionary Biology, vol.4, issue.1, p.18, 2004.
DOI : 10.1186/1471-2148-4-18

R. Juhala, M. Ford, R. Duda, A. Youlton, G. Hatfull et al., Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages, Journal of Molecular Biology, vol.299, issue.1, pp.27-51, 2000.
DOI : 10.1006/jmbi.2000.3729

S. Julio, D. Heithoff, and M. Mahan, ssrA (tmRNA) Plays a Role in Salmonella enterica Serovar Typhimurium Pathogenesis, Journal of Bacteriology, vol.182, issue.6, pp.1558-1563, 2000.
DOI : 10.1128/JB.182.6.1558-1563.2000

A. King, E. Lefkowitz, M. Adams, and E. Carstens, Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses, 2011.

P. Kourilsky, Lysogenization by bacteriophage lambda, MGG Molecular & General Genetics, vol.254, issue.2, pp.183-195, 1973.
DOI : 10.1007/BF00435190

C. Kroger, S. Dillon, and A. Cameron, The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium, Proceedings of the National Academy of Sciences, vol.109, issue.20, pp.1277-1286
DOI : 10.1073/pnas.1201061109

S. Labrie, J. Samson, and S. Moineau, Bacteriophage resistance mechanisms, Nature Reviews Microbiology, vol.153, issue.5, pp.317-327, 2010.
DOI : 10.1038/nrmicro2315

W. Lathe, B. Snel, and P. Bork, Gene context conservation of a higher order than operons, Trends in Biochemical Sciences, vol.25, issue.10, pp.474-479, 2000.
DOI : 10.1016/S0968-0004(00)01663-7

R. Lavigne, P. Darius, E. Summer, D. Seto, P. Mahadevan et al., Classification of Myoviridae bacteriophages using protein sequence similarity, BMC Microbiology, vol.9, issue.1, p.224, 2009.
DOI : 10.1186/1471-2180-9-224

J. Lawrence and H. Hendrickson, Lateral gene transfer: when will adolescence end?, Molecular Microbiology, vol.8, issue.3, pp.739-749, 2003.
DOI : 10.1046/j.1365-2958.2003.03778.x

S. Lee, S. Bailey, and D. Apirion, Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA, J Bacteriol, vol.133, pp.1015-1023, 1978.

O. Levy, J. Ptacin, P. Pease, J. Gore, M. Eisen et al., Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase, Proceedings of the National Academy of Sciences, vol.102, issue.49, pp.17618-17623, 2005.
DOI : 10.1073/pnas.0508932102

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Prophinder: a computational tool for prophage prediction in prokaryotic genomes, Bioinformatics, vol.24, issue.6, pp.863-865, 2008.
DOI : 10.1093/bioinformatics/btn043

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes, Molecular Biology and Evolution, vol.25, issue.4, pp.762-777, 2008.
DOI : 10.1093/molbev/msn023

T. Lowe and S. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

P. Mackiewicz, J. Zakrzewska-czerwinska, A. Zawilak, M. Dudek, and S. Cebrat, Where does bacterial replication start? Rules for predicting the oriC region, Nucleic Acids Research, vol.32, issue.13, pp.3781-3791, 2004.
DOI : 10.1093/nar/gkh699

T. Mcdaniel, K. Jarvis, M. Donnenberg, and J. Kaper, A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens., Proceedings of the National Academy of Sciences, vol.92, issue.5, pp.1664-1668, 1995.
DOI : 10.1073/pnas.92.5.1664

J. Meile, R. Mercier, M. Stouf, C. Pages, J. Bouet et al., The terminal region of the E. coli chromosome localises at the periphery of the nucleoid, BMC Microbiology, vol.11, issue.1, p.28, 2011.
DOI : 10.1186/1471-2180-11-28
URL : https://hal.archives-ouvertes.fr/hal-00610866

R. Mercier, M. Petit, S. Schbath, S. Robin, E. Karoui et al., The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain, Cell, vol.135, issue.3, pp.475-485, 2008.
DOI : 10.1016/j.cell.2008.08.031
URL : https://hal.archives-ouvertes.fr/hal-01197588

K. Mizuuchi, Transpositional Recombination: Mechanistic Insights from Studies of Mu and Other Elements, Annual Review of Biochemistry, vol.61, issue.1, pp.1011-1051, 1992.
DOI : 10.1146/annurev.bi.61.070192.005051

P. Mmolawa, H. Schmieger, and M. Heuzenroeder, Bacteriophage ST64B, a Genetic Mosaic of Genes from Diverse Sources Isolated from Salmonella enterica Serovar Typhimurium DT 64, Journal of Bacteriology, vol.185, issue.21, pp.6481-6485, 2003.
DOI : 10.1128/JB.185.21.6481-6485.2003

M. Napolitano, S. Almagro-moreno, and E. Boyd, Dichotomy in the evolution of pathogenicity island and bacteriophage encoded integrases from pathogenic Escherichia coli strains, Infection, Genetics and Evolution, vol.11, issue.2, pp.423-436, 2011.
DOI : 10.1016/j.meegid.2010.12.003

S. Nechaev and K. Severinov, The elusive object of desire???Interactions of bacteriophages and their hosts, Current Opinion in Microbiology, vol.11, issue.2, pp.186-193, 2008.
DOI : 10.1016/j.mib.2008.02.009

S. Nunes-duby, H. Kwon, R. 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

M. Ohnishi, K. Kurokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol, pp.481-485, 2001.

J. Peters and N. Craig, Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE, Genes & Development, vol.15, issue.6, pp.737-747, 2001.
DOI : 10.1101/gad.870201

M. Ptashne, Genetic switch: phage lambda and higher organisms, 1992.

R. Raghavan, E. Groisman, and H. Ochman, Genome-wide detection of novel regulatory RNAs in E. coli, Genome Research, vol.21, issue.9, pp.1487-1497, 2011.
DOI : 10.1101/gr.119370.110

N. Ravin, N15: The linear phage???plasmid, Plasmid, vol.65, issue.2, pp.102-109, 2011.
DOI : 10.1016/j.plasmid.2010.12.004

A. Reyes, M. Haynes, N. Hanson, F. Angly, A. Heath et al., Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.11, issue.7304, pp.334-338, 2010.
DOI : 10.1038/nature09199

R. Reyes-lamothe, X. Wang, and D. Sherratt, Escherichia coli and its chromosome, Trends in Microbiology, vol.16, issue.5, pp.238-245, 2008.
DOI : 10.1016/j.tim.2008.02.003

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics, vol.16, issue.6, pp.276-277, 2000.
DOI : 10.1016/S0168-9525(00)02024-2

E. Rocha, Order and disorder in bacterial genomes, Current Opinion in Microbiology, vol.7, issue.5, pp.519-527, 2004.
DOI : 10.1016/j.mib.2004.08.006

E. Rocha, The Organization of the Bacterial Genome, Annual Review of Genetics, vol.42, issue.1, pp.211-233, 2008.
DOI : 10.1146/annurev.genet.42.110807.091653

E. Rocha and A. Danchin, Essentiality, not expressiveness, drives gene-strand bias in bacteria, Nature Genetics, vol.34, issue.4, pp.377-378, 2003.
DOI : 10.1038/ng1209

F. Rohwer and R. Edwards, The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage, Journal of Bacteriology, vol.184, issue.16, pp.4529-4535, 2002.
DOI : 10.1128/JB.184.16.4529-4535.2002

M. Roossinck, The good viruses: viral mutualistic symbioses, Nature Reviews Microbiology, vol.42, issue.2, pp.99-108, 2011.
DOI : 10.1038/nrmicro2491

S. Schbath, An Efficient Statistic to Detect Over- and Under-represented Words in DNA Sequences, Journal of Computational Biology, vol.4, issue.2, pp.189-192, 1997.
DOI : 10.1089/cmb.1997.4.189

H. Schmidt, K. Strimmer, M. Vingron, V. Haeseler, and A. , TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502

V. Scolari, B. Bassetti, B. Sclavi, and M. Lagomarsino, Gene clusters reflecting macrodomain structure respond to nucleoid perturbations, Mol. BioSyst., vol.25, issue.11, pp.878-888, 2011.
DOI : 10.1039/C0MB00213E

S. Shinedling, D. Parma, and L. Gold, Wild-type bacteriophage T4 is restricted by the lambda rex genes, J Virol, vol.61, pp.3790-3794, 1987.

A. Shinhara, M. Matsui, K. Hiraoka, W. Nomura, R. Hirano et al., Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli, BMC Genomics, vol.23, issue.1, p.428, 2011.
DOI : 10.1186/1471-2164-12-428

E. Six and C. Klug, Bacteriophage P4: a satellite virus depending on a helper such as prophage P2, Virology, vol.51, issue.2, pp.327-344, 1973.
DOI : 10.1016/0042-6822(73)90432-7

M. Smith and H. Thorpe, Diversity in the serine recombinases, Molecular Microbiology, vol.82, issue.2, pp.299-307, 2002.
DOI : 10.1046/j.1365-2958.2002.02891.x

B. Snel, M. Huynen, and B. Dutilh, GENOME TREES AND THE NATURE OF GENOME EVOLUTION, Annual Review of Microbiology, vol.59, issue.1, pp.191-209, 2005.
DOI : 10.1146/annurev.micro.59.030804.121233

F. St-pierre and D. Endy, Determination of cell fate selection during phage lambda infection, Proceedings of the National Academy of Sciences, vol.105, issue.52, pp.20705-20710, 2008.
DOI : 10.1073/pnas.0808831105

C. Suttle, Viruses in the sea, Nature, vol.155, issue.7057, pp.356-361, 2005.
DOI : 10.1006/viro.2001.1028

O. Tenaillon, D. Skurnik, B. Picard, and E. Denamur, The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-224, 2010.
DOI : 10.1038/nrmicro2298

N. Thomson, S. Baker, and D. Pickard, The Role of Prophage-like Elements in the Diversity of Salmonella enterica Serovars, Journal of Molecular Biology, vol.339, issue.2, pp.279-300, 2004.
DOI : 10.1016/j.jmb.2004.03.058

M. Touchon, C. Hoede, and O. Tenaillon, Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009.
DOI : 10.1371/journal.pgen.1000344.s016
URL : https://hal.archives-ouvertes.fr/hal-00390293

M. Touchon and E. 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

M. Touchon and E. Rocha, The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella, PLoS ONE, vol.14, issue.6, p.11126, 2010.
DOI : 10.1371/journal.pone.0011126.s006
URL : https://hal.archives-ouvertes.fr/pasteur-01374940

F. Touzain, M. Petit, S. Schbath, E. Karoui, and M. , DNA motifs that sculpt the bacterial chromosome, Nature Reviews Microbiology, vol.15, issue.1, pp.15-26, 2011.
DOI : 10.1038/nrmicro2477
URL : https://hal.archives-ouvertes.fr/hal-01019344

M. Val, O. Skovgaard, M. Ducos-galand, M. Bland, and D. Mazel, Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues, PLoS Genetics, vol.163, issue.1, p.1002472, 2012.
DOI : 10.1371/journal.pgen.1002472.s005
URL : https://hal.archives-ouvertes.fr/inserm-01285625

M. Valens, S. Penaud, M. Rossignol, F. Cornet, and F. Boccard, Macrodomain organization of the Escherichia coli chromosome, The EMBO Journal, vol.241, issue.21, pp.4330-4341, 2004.
DOI : 10.1038/sj.emboj.7600028

L. Van-melderen, S. De-bast, and M. , Bacterial Toxin???Antitoxin Systems: More Than Selfish Entities?, PLoS Genetics, vol.25, issue.3, p.1000437, 2009.
DOI : 10.1371/journal.pgen.1000437.t002

G. Vernikos, N. Thomson, and J. Parkhill, Genetic flux over time in the Salmonella lineage, Genome Biology, vol.8, issue.6, p.100, 2007.
DOI : 10.1186/gb-2007-8-6-r100

H. Wang, C. Yang, G. Lee, F. Chang, H. Wilson et al., Integration specificities of two lambdoid phages (21 and e14) that insert at the same attB site., Journal of Bacteriology, vol.179, issue.18, pp.5705-5711, 1997.
DOI : 10.1128/jb.179.18.5705-5711.1997

K. Wassarman, F. Repoila, C. Rosenow, G. Storz, and S. Gottesman, Identification of novel small RNAs using comparative genomics and microarrays, Genes & Development, vol.15, issue.13, pp.1637-1651, 2001.
DOI : 10.1101/gad.901001

L. Waters and G. Storz, Regulatory RNAs in Bacteria, Cell, vol.136, issue.4, pp.615-628, 2009.
DOI : 10.1016/j.cell.2009.01.043

M. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiology Reviews, vol.28, issue.2, pp.127-181, 2004.
DOI : 10.1016/j.femsre.2003.08.001

P. Wiggins, K. Cheveralls, J. Martin, R. Lintner, and J. Kondev, Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament, Proceedings of the National Academy of Sciences, vol.107, issue.11, pp.4991-4995, 2010.
DOI : 10.1073/pnas.0912062107

K. Williams, Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies, Nucleic Acids Research, vol.30, issue.4, pp.866-875, 2002.
DOI : 10.1093/nar/30.4.866

K. Williams, Traffic at the tmRNA Gene, Journal of Bacteriology, vol.185, issue.3, pp.1059-1070, 2003.
DOI : 10.1128/JB.185.3.1059-1070.2003

C. Winstanley, M. Langille, and J. Fothergill, Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa, Genome Research, vol.19, issue.1, pp.12-23, 2008.
DOI : 10.1101/gr.086082.108

M. Withers, L. Wernisch, and M. Dos-reis, Archaeology and evolution of transfer RNA genes in the Escherichia coli genome, RNA, vol.12, issue.6, pp.933-942, 2006.
DOI : 10.1261/rna.2272306

Y. Wolf, I. Rogozin, N. Grishin, and E. Koonin, Genome trees and the tree of life, Trends in Genetics, vol.18, issue.9, pp.472-479, 2002.
DOI : 10.1016/S0168-9525(02)02744-0

A. Zaslaver, A. Mayo, M. Ronen, and U. Alon, Optimal gene partition into operons correlates with gene functional order, Physical Biology, vol.3, issue.3, pp.183-189, 2006.
DOI : 10.1088/1478-3975/3/3/003

Y. Zhou, Y. Liang, K. Lynch, J. Dennis, and D. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.39, issue.suppl, pp.347-352, 2011.
DOI : 10.1093/nar/gkr485