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

M. Breitbart and F. Rohwer, Here a virus, there a virus, everywhere the same virus?, Trends in Microbiology, vol.13, issue.6, pp.278-284, 2005.
DOI : 10.1016/j.tim.2005.04.003

D. Krüger and T. Bickle, Bacteriophage survival Multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts, Microbiol Rev, vol.47, pp.345-360, 1983.

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, and P. Boyaval, CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1712, 2007.
DOI : 10.1126/science.1138140

H. Deveau, R. Barrangou, J. Garneau, J. Labonte, and C. Fremaux, Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus, Journal of Bacteriology, vol.190, issue.4, pp.1390-1400, 2008.
DOI : 10.1128/JB.01412-07

P. Horvath, D. Romero, A. Coute-monvoisin, M. Richards, and H. Deveau, Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus, Journal of Bacteriology, vol.190, issue.4, pp.1401-1412, 2008.
DOI : 10.1128/JB.01415-07

L. Marraffini and E. Sontheimer, Self versus non-self discrimination during CRISPR RNA-directed immunity, Nature, vol.35, issue.7280, pp.568-571, 2010.
DOI : 10.1038/nature08703

R. Jansen, J. Embden, W. Gaastra, and L. Schouls, Identification of genes that are associated with DNA repeats in prokaryotes, Molecular Microbiology, vol.43, issue.6, pp.1565-1575, 2002.
DOI : 10.1128/JB.182.9.2393-2401.2000

R. Sorek, V. Kunin, and P. Hugenholtz, 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

J. Van-der-oost, M. Jore, E. Westra, M. Lundgren, and S. Brouns, CRISPR-based adaptive and heritable immunity in prokaryotes, Trends in Biochemical Sciences, vol.34, issue.8, pp.401-407, 2009.
DOI : 10.1016/j.tibs.2009.05.002

V. Kunin, R. Sorek, and P. Hugenholtz, Evolutionary conservation of sequence and secondary structures in CRISPR repeats, Genome Biology, vol.8, issue.4, p.61, 2007.
DOI : 10.1186/gb-2007-8-4-r61

D. Haft, J. Selengut, E. Mongodin, and K. Nelson, A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes, PLoS Computational Biology, vol.21, issue.6, p.60, 2005.
DOI : 1367-4803(2005)021[0293:GPASFT]2.0.CO;2

K. Makarova, N. Grishin, S. Shabalina, Y. Wolf, and E. Koonin, A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biology Direct, vol.1, issue.1, p.7, 2006.
DOI : 10.1186/1745-6150-1-7

R. Lillestol, S. Shah, K. Brugger, P. Redder, and H. Phan, CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties, Molecular Microbiology, vol.190, issue.1, pp.259-272, 2009.
DOI : 10.1111/j.1365-2958.2009.06641.x

C. Hale, K. Kleppe, R. Terns, and M. Terns, Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus, RNA, vol.14, issue.12, pp.2572-2579, 2008.
DOI : 10.1261/rna.1246808

A. Bolotin, B. Quinquis, A. Sorokin, and S. Ehrlich, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, vol.151, pp.2551-2561, 2005.

F. Mojica, C. Diez-villasenor, J. Garcia-martinez, and E. Soria, Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements, Journal of Molecular Evolution, vol.2, issue.2, pp.174-182, 2005.
DOI : 10.1007/s00239-004-0046-3

C. Pourcel, G. Salvignol, and G. Vergnaud, CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, vol.151, pp.653-663, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01158317

P. Horvath, A. Coute-monvoisin, D. Romero, P. Boyaval, and C. Fremaux, Comparative analysis of CRISPR loci in lactic acid bacteria genomes, International Journal of Food Microbiology, vol.131, issue.1, 2009.
DOI : 10.1016/j.ijfoodmicro.2008.05.030

S. Brouns, M. Jore, M. Lundgren, E. Westra, and R. Slijkhuis, Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes, Science, vol.321, issue.5891, pp.960-964, 2008.
DOI : 10.1126/science.1159689

L. Marraffini and E. Sontheimer, CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA, Science, vol.322, issue.5909, pp.1843-1845, 2008.
DOI : 10.1126/science.1165771

U. Dobrindt, (Patho-)Genomics of Escherichia coli, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.357-371, 2005.
DOI : 10.1016/j.ijmm.2005.07.009

Y. Ishino, H. Shinagawa, K. Makino, M. Amemura, and A. Nakata, Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product., Journal of Bacteriology, vol.169, issue.12, pp.5429-5433, 1987.
DOI : 10.1128/jb.169.12.5429-5433.1987

M. Vulic, F. Dionisio, F. Taddei, and M. Radman, Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria, Proceedings of the National Academy of Sciences, vol.94, issue.18, pp.9763-9767, 1997.
DOI : 10.1073/pnas.94.18.9763

M. Touchon, C. Hoede, O. Tenaillon, V. Barbe, and S. Baeriswyl, 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

F. Yang, Y. J. Zhang, X. Chen, L. Jiang, and Y. , Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery, Nucleic Acids Research, vol.33, issue.19, pp.6445-6458, 2005.
DOI : 10.1093/nar/gki954

E. Lerat and H. Ochman, ??-??: Exploring the outer limits of bacterial pseudogenes, Genome Research, vol.14, issue.11, pp.2273-2278, 2004.
DOI : 10.1101/gr.2925604

K. Balbi, E. Rocha, and E. Feil, The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp., Molecular Biology and Evolution, vol.26, issue.2, pp.345-355, 2009.
DOI : 10.1093/molbev/msn252

U. Pul, R. Wurm, Z. Arslan, R. Geißen, and N. Hofmann, promoters and their silencing by H-NS, Molecular Microbiology, vol.15, issue.6, pp.1495-1512, 2010.
DOI : 10.1111/j.1365-2958.2010.07073.x

D. Andersson and D. Hughes, Gene Amplification and Adaptive Evolution in Bacteria, Annual Review of Genetics, vol.43, issue.1, pp.167-195, 2009.
DOI : 10.1146/annurev-genet-102108-134805

T. Wirth, D. Falush, R. Lan, F. Colles, and P. Mensa, Sex and virulence in Escherichia coli: an evolutionary perspective, Molecular Microbiology, vol.179, issue.5, pp.1136-1151, 2006.
DOI : 10.1111/j.1365-2958.2005.04985.x

URL : https://hal.archives-ouvertes.fr/hal-00174910

M. Savageau, Escherichia coli Habitats, Cell Types, and Molecular Mechanisms of Gene Control, The American Naturalist, vol.122, issue.6, pp.732-744, 1983.
DOI : 10.1086/284168

E. Rocha, J. Smith, L. Hurst, M. Holden, and J. Cooper, Comparisons of dN/dS are time dependent for closely related bacterial genomes, Journal of Theoretical Biology, vol.239, issue.2, pp.226-235, 2006.
DOI : 10.1016/j.jtbi.2005.08.037

S. Shah, N. Hansen, and R. Garrett, Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism, Biochemical Society Transactions, vol.37, issue.1, pp.23-28, 2009.
DOI : 10.1042/BST0370023

I. Kobayashi, Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution, Nucleic Acids Research, vol.29, issue.18, pp.3742-3756, 2001.
DOI : 10.1093/nar/29.18.3742

A. Nakata, M. Amemura, and K. Makino, Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome., Journal of Bacteriology, vol.171, issue.6, pp.3553-3556, 1989.
DOI : 10.1128/jb.171.6.3553-3556.1989

F. Mojica, C. Diez-villasenor, J. Garcia-martinez, and C. Almendros, Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, vol.155, pp.733-740, 2009.

J. Zhang, E. Abadia, G. Refregier, S. Tafaj, and M. Boschiroli, Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay, Journal of Medical Microbiology, vol.59, issue.3, pp.285-294, 2010.
DOI : 10.1099/jmm.0.016949-0

URL : https://hal.archives-ouvertes.fr/hal-00527223

E. Price, H. Smith, F. Huygens, and P. Giffard, High-Resolution DNA Melt Curve Analysis of the Clustered, Regularly Interspaced Short-Palindromic-Repeat Locus of Campylobacter jejuni, Applied and Environmental Microbiology, vol.73, issue.10, pp.3431-3436, 2007.
DOI : 10.1128/AEM.02702-06

F. Rodriguez-valera, A. Martin-cuadrado, B. Rodriguez-brito, L. Pasic, and T. Thingstad, Explaining microbial population genomics through phage predation, Nature Reviews Microbiology, vol.62, issue.11, pp.828-836, 2009.
DOI : 10.1038/nrmicro2235

E. Rocha, An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction, Genome Research, vol.13, issue.6, pp.1123-1132, 2003.
DOI : 10.1101/gr.966203

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

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

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

H. Schmidt, K. Strimmer, M. Vingron, and A. Von-haeseler, 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

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

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

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

C. Bland, T. Ramsey, F. Sabree, M. Lowe, and K. Brown, CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, vol.8, issue.1, p.209, 2007.
DOI : 10.1186/1471-2105-8-209

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

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595

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