C. Ple, strains: Reverse engineering development of an anti-inflammatory cheese, Molecular Nutrition & Food Research, vol.2015, issue.4, pp.935-948201500580, 2016.
DOI : 10.1128/AEM.01360-15

S. Rocha and C. , Local and Systemic Immune Mechanisms Underlying the Anti-Colitis Effects of the Dairy Bacterium Lactobacillus delbrueckii, PLoS ONE, vol.7, issue.1, p.85923, 2014.
DOI : 10.1371/journal.pone.0085923.g006

URL : https://hal.archives-ouvertes.fr/hal-01204288

S. Rocha and C. , Anti-inflammatory properties of dairy lactobacilli, Inflammatory Bowel Diseases, vol.18, issue.4, pp.657-666, 2012.
DOI : 10.1002/ibd.21834

URL : https://hal.archives-ouvertes.fr/hal-00632487

E. Kafsi and H. , Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action, BMC Genomics, vol.15, issue.1, pp.10-1186, 2014.
DOI : 10.1186/1471-2164-15-407

URL : https://hal.archives-ouvertes.fr/pasteur-01017376

M. Van-de-guchte, The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution, Proceedings of the National Academy of Sciences, vol.299, issue.4, pp.9274-9279, 2006.
DOI : 10.1006/jmbi.2000.3787

P. J. Lai, Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands, Genes to Cells, vol.580, issue.2, pp.136-145, 2016.
DOI : 10.1111/gtc.12326

D. R. Leach, Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair, BioEssays, vol.55, issue.12, pp.893-900, 1994.
DOI : 10.1002/bies.950161207

P. L. Kuempel, J. M. Henson, L. Dircks, M. Tecklenburg, and D. F. Lim, dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli, New Biol, vol.3, pp.799-811, 1991.

W. W. Steiner and P. L. Kuempel, Sister chromatid exchange frequencies in Escherichia coli analyzed by recombination at the dif resolvase site, J Bacteriol, vol.180, pp.6269-6275, 1998.

L. Aussel, FtsK Is a DNA Motor Protein that Activates Chromosome Dimer Resolution by Switching the Catalytic State of the XerC and XerD Recombinases, Cell, vol.108, issue.2, pp.195-205, 2002.
DOI : 10.1016/S0092-8674(02)00624-4

X. Didelot and D. Falush, Inference of Bacterial Microevolution Using Multilocus Sequence Data, Genetics, vol.175, issue.3, pp.1251-1266, 2007.
DOI : 10.1534/genetics.106.063305

T. Uchida, N. Ishihara, H. Zenitani, K. Hiratsu, and H. Kinashi, Circularized Chromosome with a Large Palindromic Structure in Streptomyces griseus Mutants, Journal of Bacteriology, vol.186, issue.11, pp.3313-3320, 2004.
DOI : 10.1128/JB.186.11.3313-3320.2004

E. Darmon, E. coli SbcCD and RecA Control Chromosomal Rearrangement Induced by an Interrupted Palindrome, Molecular Cell, vol.39, issue.1, pp.59-70011, 2010.
DOI : 10.1016/j.molcel.2010.06.011

URL : https://hal.archives-ouvertes.fr/inserm-00192323

P. Nicolas, P. Bessieres, S. D. Ehrlich, E. Maguin, and M. Van-de-guchte, Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract, BMC Evolutionary Biology, vol.7, issue.1, p.141, 2007.
DOI : 10.1186/1471-2148-7-141

J. A. Eisen, J. F. Heidelberg, O. White, and S. L. Salzberg, Evidence for symmetric chromosomal inversions around the replication origin in bacteria, Genome, vol.1, pp.10-1186, 2000.

P. Mackiewicz, D. Mackiewicz, M. Kowalczuk, and S. Cebrat, Flip-flop around the origin and terminus of replication in prokaryotic genomes, Genome biology, vol.2, p.1004, 2001.

D. Canceill and S. D. Ehrlich, Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli., Proceedings of the National Academy of Sciences, vol.93, issue.13, pp.6647-6652, 1996.
DOI : 10.1073/pnas.93.13.6647

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC39080

S. K. Deng, Y. Yin, T. D. Petes, and L. S. Symington, Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification, Molecular Cell, vol.60, issue.3, pp.500-508, 2015.
DOI : 10.1016/j.molcel.2015.09.027

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636734

H. Tanaka, Intrastrand Annealing Leads to the Formation of a Large DNA Palindrome and Determines the Boundaries of Genomic Amplification in Human Cancer, Molecular and Cellular Biology, vol.27, issue.6, pp.10-112801313, 1993.
DOI : 10.1128/MCB.01313-06

H. Tanaka, S. J. Tapscott, B. J. Trask, and M. C. Yao, Short inverted repeats initiate gene amplification through the formation of a large DNA palindrome in mammalian cells, Proceedings of the National Academy of Sciences, vol.8, issue.6, pp.8772-8777, 2002.
DOI : 10.1016/S1097-2765(01)00425-7

A. J. Rattray, B. K. Shafer, B. Neelam, and J. N. Strathern, A mechanism of palindromic gene amplification in Saccharomyces cerevisiae, Genes & Development, vol.19, issue.11, pp.1390-1399, 2005.
DOI : 10.1101/gad.1315805

B. Michel, Rescue of arrested replication forks by homologous recombination, Proceedings of the National Academy of Sciences, vol.113, issue.15, pp.8181-8188111008798, 2001.
DOI : 10.1006/jmbi.1999.2847

J. Corre and J. M. Louarn, Evidence from Terminal Recombination Gradients that FtsK Uses Replichore Polarity To Control Chromosome Terminus Positioning at Division in Escherichia coli, Journal of Bacteriology, vol.184, issue.14, pp.3801-3807, 2002.
DOI : 10.1128/JB.184.14.3801-3807.2002

E. C. Hendricks, H. Szerlong, T. Hill, and P. Kuempel, Cell division, guillotining of dimer chromosomes and SOS induction in resolution mutants (dif, xerC and xerD) of Escherichia coli, Molecular Microbiology, vol.173, issue.4, pp.973-981, 2000.
DOI : 10.1016/0923-2508(91)90046-D

C. Lesterlin, F. X. Barre, and F. Cornet, Genetic recombination and the cell cycle: what we have learned from chromosome dimers, Molecular Microbiology, vol.180, issue.5, pp.1151-1160, 2004.
DOI : 10.1111/j.1365-2958.2004.04356.x

J. Prikryl, E. C. Hendricks, and P. L. Kuempel, DNA degradation in the terminus region of resolvase mutants of Escherichia coli, and suppression of this degradation and the Dif phenotype by recD, Biochimie, vol.83, issue.2, pp.171-176, 2001.
DOI : 10.1016/S0300-9084(00)01221-9

A. M. Albertini, M. Hofer, M. P. Calos, and J. H. Miller, On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions, Cell, vol.29, issue.2, pp.319-328, 1982.
DOI : 10.1016/0092-8674(82)90148-9

A. I. Nilsson, From The Cover: Bacterial genome size reduction by experimental evolution, Proceedings of the National Academy of Sciences, vol.95, issue.16, pp.12112-121160503654102, 2005.
DOI : 10.1073/pnas.95.16.9413

L. A. Matthews and L. A. Simmons, Bacterial Nonhomologous End Joining Requires Teamwork, Journal of Bacteriology, vol.196, issue.19, pp.3363-336502042, 1128.
DOI : 10.1128/JB.02042-14

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187666

A. L. Hughes, Near Neutrality, Annals of the New York Academy of Sciences, vol.312, issue.1, pp.162-179, 2008.
DOI : 10.1196/annals.1438.001

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707937

M. Kimura, Evolutionary Rate at the Molecular Level, Nature, vol.16, issue.5129, pp.624-626, 1968.
DOI : 10.1038/217624a0

E. Kafsi and H. , Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties, Genome Announcements, vol.2, issue.4, pp.10-1128, 2014.
DOI : 10.1128/genomeA.00328-14

URL : https://hal.archives-ouvertes.fr/hal-01204323

K. Makarova, Comparative genomics of the lactic acid bacteria, Proceedings of the National Academy of Sciences, vol.29, issue.1, pp.15611-15616, 2006.
DOI : 10.1093/nar/29.1.22

P. Hao, 44331 | DOI: 10.1038/srep44331 34 Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production, PLoS One, vol.7, issue.6, p.15964, 2011.

Z. Sun, Complete Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus Strain ND02, Journal of Bacteriology, vol.193, issue.13, pp.3426-3427, 2011.
DOI : 10.1128/JB.05004-11

H. Chiapello, MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level, BMC Bioinformatics, vol.9, issue.1, p.498, 2008.
DOI : 10.1186/1471-2105-9-498

URL : https://hal.archives-ouvertes.fr/hal-00489678

H. Devillers, H. Chiapello, S. Schbath, and M. E. Karoui, Robustness Assessment of Whole Bacterial Genome Segmentations, Journal of Computational Biology, vol.18, issue.9, pp.1155-1165, 2011.
DOI : 10.1089/cmb.2011.0115

URL : https://hal.archives-ouvertes.fr/hal-00999893

S. Guindon, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

T. M. Keane, C. J. Creevey, M. M. Pentony, T. J. Naughton, and J. Mclnerney, Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified, BMC evolutionary biology 6, vol.29, pp.10-1186, 2006.

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

G. A. Watterson, On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975.
DOI : 10.1016/0040-5809(75)90020-9

A. Gelman and D. B. Rubin, Inference from Iterative Simulation Using Multiple Sequences, Statistical Science, vol.7, issue.4, pp.457-472, 1992.
DOI : 10.1214/ss/1177011136

G. Achaz, F. Boyer, E. P. Rocha, A. Viari, and E. Coissac, Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics, vol.23, issue.1, pp.119-121, 2007.
DOI : 10.1093/bioinformatics/btl519

P. Mackiewicz, J. Zakrzewska-czerwinska, A. Zawilak, M. R. 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

J. Lobry, Asymmetric substitution patterns in the two DNA strands of bacteria, Molecular Biology and Evolution, vol.13, issue.5, pp.660-665, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025626

URL : https://hal.archives-ouvertes.fr/hal-00435031