S. Gottesman and G. Storz, Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations, Cold Spring Harbor Perspectives in Biology, vol.3, issue.12, 2011.
DOI : 10.1101/cshperspect.a003798

URL : http://cshperspectives.cshlp.org/content/3/12/a003798.full.pdf

S. Modi, D. Camacho, M. Kohanski, G. Walker, and J. Collins, Functional characterization of bacterial sRNAs using a network biology approach, Proceedings of the National Academy of Sciences, vol.301, issue.5629, pp.15522-15529, 2011.
DOI : 10.1126/science.1081900

P. Mandin and M. Guillier, Expanding control in bacteria: interplay between small RNAs and transcriptional regulators to control gene expression, Current Opinion in Microbiology, vol.16, issue.2, pp.125-157, 2013.
DOI : 10.1016/j.mib.2012.12.005

URL : https://hal.archives-ouvertes.fr/hal-00823497

I. Caldelari, Y. Chao, P. Romby, and J. Vogel, RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med, p.10298, 2013.

A. Toledo-arana, O. Dussurget, G. Nikitas, N. Sesto, H. Guet-revillet et al., The Listeria transcriptional landscape from saprophytism to virulence, Nature, vol.99, issue.7249, pp.950-956, 2009.
DOI : 10.1016/S1438-4221(00)80086-7

A. Peer and H. Margalit, Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions, Journal of Bacteriology, vol.193, issue.7, pp.1690-701, 2011.
DOI : 10.1128/JB.01419-10

URL : http://jb.asm.org/content/193/7/1690.full.pdf

A. Richter and R. Backofen, Accessibility and conservation: General features of bacterial small RNA???mRNA interactions?, RNA Biology, vol.6, issue.7, pp.954-65, 2012.
DOI : 10.1186/1748-7188-6-3

C. Beisel, T. Updegrove, B. Janson, and G. Storz, Multiple factors dictate target selection by Hfq-binding small RNAs, The EMBO Journal, vol.31, issue.8, pp.1961-74, 2012.
DOI : 10.1093/nar/gkg595

URL : http://emboj.embopress.org/content/embojnl/31/8/1961.full.pdf

P. Wright, A. Richter, K. Papenfort, M. Mann, J. Vogel et al., Comparative genomics boosts target prediction for bacterial small RNAs, Proceedings of the National Academy of Sciences, vol.41, issue.D1, pp.3487-96, 2013.
DOI : 10.1093/nar/gks1027

URL : http://www.pnas.org/content/110/37/E3487.full.pdf

T. Updegrove, S. Shabalina, and G. Storz, How do base-pairing small RNAs evolve?, FEMS Microbiology Reviews, vol.425, issue.3, pp.379-91, 2015.
DOI : 10.1016/j.jmb.2013.01.006

URL : https://academic.oup.com/femsre/article-pdf/39/3/379/17051672/fuv014.pdf

R. Raghavan, E. Groisman, and H. Ochman, Genome-wide detection of novel regulatory RNAs in E. coli, Genome Research, vol.21, issue.9, pp.1487-97, 2011.
DOI : 10.1101/gr.119370.110

C. Kröger, S. Dillon, A. Cameron, K. Papenfort, S. Sivasankaran et al., The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium, Proceedings of the National Academy of Sciences, vol.36, issue.6, pp.1277-86, 2012.
DOI : 10.1093/nar/gkn050

I. Irnov, C. Sharma, J. Vogel, and W. Winkler, Identification of regulatory RNAs in Bacillus subtilis, Nucleic Acids Research, vol.34, issue.19, pp.6637-51, 2010.
DOI : 10.1111/j.1574-6976.2009.00199.x

R. Mars, P. Nicolas, M. Ciccolini, E. Reilman, A. Reder et al., Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis, PLOS Genetics, vol.81, issue.25, p.1005046, 2015.
DOI : 10.1371/journal.pgen.1005046.s013

J. Mellin, M. Koutero, D. Dar, M. Nahori, R. Sorek et al., Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA, Science, vol.3, issue.12, pp.940-943, 2014.
DOI : 10.1101/cshperspect.a003798

URL : https://hal.archives-ouvertes.fr/pasteur-01120664

J. Mellin, T. Tiensuu, C. Bécavin, E. Gouin, J. Johansson et al., A riboswitch-regulated antisense RNA in Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.109, issue.41, pp.13132-13139, 2013.
DOI : 10.1073/pnas.1212809109

J. Christiansen, J. Nielsen, T. Ebersbach, P. Valentin-hansen, L. Søgaard-andersen et al., Identification of small Hfq-binding RNAs in Listeria monocytogenes, RNA, vol.12, issue.7, pp.1383-96, 2006.
DOI : 10.1261/rna.49706

P. Mandin, F. Repoila, M. Vergassola, T. Geissmann, and P. Cossart, Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Research, vol.149, issue.3, pp.962-74, 2007.
DOI : 10.1099/mic.0.26003-0

URL : https://hal.archives-ouvertes.fr/hal-00129258

H. Oliver, R. Orsi, L. Ponnala, U. Keich, W. Wang et al., Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs, BMC Genomics, vol.10, issue.1, p.641, 2009.
DOI : 10.1186/1471-2164-10-641

M. Mraheil, A. Billion, W. Mohamed, K. Mukherjee, C. Kuenne et al., The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages, Nucleic Acids Research, vol.139, issue.10, pp.4235-4283, 2011.
DOI : 10.1016/j.cell.2009.08.046

O. Wurtzel, N. Sesto, J. Mellin, I. Karunker, S. Edelheit et al., Comparative transcriptomics of pathogenic and non-pathogenic Listeria species, Molecular Systems Biology, vol.270, p.583, 2012.
DOI : 10.1093/nar/gkm951

E. Loh, O. Dussurget, J. Gripenland, K. Vaitkevicius, T. Tiensuu et al., A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes, Cell, vol.139, issue.4, pp.770-779, 2009.
DOI : 10.1016/j.cell.2009.08.046

J. Johansson, P. Mandin, A. Renzoni, C. Chiaruttini, M. Springer et al., An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes, Cell, vol.110, issue.5, pp.551-61, 2002.
DOI : 10.1016/S0092-8674(02)00905-4

N. Sesto, M. Koutero, and P. Cossart, infection, Future Microbiology, vol.9, issue.9, pp.1025-1062, 2014.
DOI : 10.1126/science.1255083

URL : https://hal.archives-ouvertes.fr/pasteur-01161885

J. Quereda, A. Ortega, M. Pucciarelli, G. Portillo, and F. , The Listeria Small RNA Rli27 Regulates a Cell Wall Protein inside Eukaryotic Cells by Targeting a Long 5???-UTR Variant, PLoS Genetics, vol.11, issue.10, p.1004765, 2014.
DOI : 10.1371/journal.pgen.1004765.s011

Y. Peng, Q. Meng, J. Qiao, K. Xie, C. Chen et al., The Regulatory Roles of ncRNA Rli60 in Adaptability of Listeria monocytogenes to Environmental Stress and Biofilm Formation, Current Microbiology, vol.195, issue.2, pp.77-83, 2016.
DOI : 10.1007/s00203-012-0855-5

C. Toffano-nioche, A. Nguyen, C. Kuchly, A. Ott, D. Gautheret et al., Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus, RNA, vol.18, issue.12, pp.2201-2220, 2012.
DOI : 10.1261/rna.033324.112

URL : https://hal.archives-ouvertes.fr/hal-00757205

E. Skippington and M. Ragan, Evolutionary dynamics of small RNAs, p.27

A. Peer and H. Margalit, Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions, RNA, vol.20, issue.7, pp.994-1003, 2014.
DOI : 10.1261/rna.043133.113

R. Orsi and M. Wiedmann, Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009, Applied Microbiology and Biotechnology, vol.40, issue.12, pp.5273-87, 2016.
DOI : 10.1128/AEM.68.2.456-463.2002

M. Hamon, H. Bierne, and P. Cossart, Listeria monocytogenes: a multifaceted model, Nature Reviews Microbiology, vol.73, issue.6, pp.423-457, 2006.
DOI : 10.1128/IAI.73.10.6199-6209.2005

J. Pizarro-cerdá and P. Cossart, Subversion of cellular functions byListeria monocytogenes, The Journal of Pathology, vol.102, issue.2, pp.215-238, 2006.
DOI : 10.1128/9781555816513.ch53

P. Cossart, Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.22, issue.3, pp.19484-91, 2011.
DOI : 10.1016/j.smim.2010.02.002

P. Glaser, L. Frangeul, C. Buchrieser, C. Rusniok, A. Amend et al., Comparative genomics of listeria species, Science, vol.294, pp.849-52, 2001.

C. Bécavin, M. Koutero, N. Tchitchek, F. Cerutti, P. Lechat et al., ABSTRACT, mSystems, vol.2, issue.2, pp.10-112800186, 2017.
DOI : 10.1128/mSystems.00186-16

C. Bécavin, C. Bouchier, P. Lechat, C. Archambaud, S. Creno et al., Comparison of Widely Used Listeria monocytogenes Strains EGD, 10403S, and EGD-e Highlights Genomic Differences Underlying Variations in Pathogenicity, mBio, vol.5, issue.2, pp.969-983, 2014.
DOI : 10.1128/mBio.00969-14

C. Kuenne, A. Billion, M. Mraheil, A. Strittmatter, R. Daniel et al., Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome, BMC Genomics, vol.14, issue.1, p.47, 2013.
DOI : 10.1186/1471-2164-13-384.:384-13

M. Pagel, Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters, Proceedings of the Royal Society B: Biological Sciences, vol.255, issue.1342, pp.37-45, 1994.
DOI : 10.1098/rspb.1994.0006

R. Orsi, H. Bakker, and M. Wiedmann, Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics, International Journal of Medical Microbiology, vol.301, issue.2, pp.79-96, 2011.
DOI : 10.1016/j.ijmm.2010.05.002

C. Beeley, Web application with R using shiny. Packt Pub Limited, 2013.

R. Tatusov, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Research, vol.28, issue.1, pp.33-39, 2000.
DOI : 10.1093/nar/28.1.33

R. Fisher, The Logic of Inductive Inference, Journal of the Royal Statistical Society, vol.98, issue.1, p.39, 1935.
DOI : 10.2307/2342435

J. Vázquez-boland, G. Domínguez-bernal, B. González-zorn, J. Kreft, and W. Goebel, Pathogenicity islands and virulence evolution in Listeria, Microbes and Infection, vol.3, issue.7, pp.571-84, 2001.
DOI : 10.1016/S1286-4579(01)01413-7

S. Chatterjee, H. Hossain, S. Otten, C. Kuenne, K. Kuchmina et al., Intracellular Gene Expression Profile of Listeria monocytogenes, Infection and Immunity, vol.74, issue.2, pp.1323-1361, 2006.
DOI : 10.1128/IAI.74.2.1323-1338.2006

D. Cabanes, P. Dehoux, O. Dussurget, L. Frangeul, and P. Cossart, Surface proteins and the pathogenic potential of Listeria monocytogenes, Trends in Microbiology, vol.10, issue.5, pp.238-283, 2002.
DOI : 10.1016/S0966-842X(02)02342-9

C. Faralla, G. Rizzuto, D. Lowe, B. Kim, C. Cooke et al., InlP, a New Virulence Factor with Strong Placental Tropism, Infection and Immunity, vol.84, issue.12, pp.3584-96, 2016.
DOI : 10.1128/IAI.00625-16

D. Raffelsbauer, A. Bubert, F. Engelbrecht, J. Scheinpflug, A. Simm et al., The gene cluster inlC2DE of Listeria monocytogenes contains additional new internalin genes and is important for virulence in mice, Molecular and General Genetics MGG, vol.260, issue.2-3, pp.144-58, 1998.
DOI : 10.1007/s004380050880

C. Sabet, M. Lecuit, D. Cabanes, P. Cossart, and H. Bierne, LPXTG Protein InlJ, a Newly Identified Internalin Involved in Listeria monocytogenes Virulence, Infection and Immunity, vol.73, issue.10, pp.6912-6934, 2005.
DOI : 10.1128/IAI.73.10.6912-6922.2005

A. Lebreton, G. Lakisic, V. Job, L. Fritsch, T. Tham et al., A Bacterial Protein Targets the BAHD1 Chromatin Complex to Stimulate Type III Interferon Response, Science, vol.11, issue.6, pp.1319-1340, 2011.
DOI : 10.1111/j.1469-0691.2005.01146.x

URL : https://hal.archives-ouvertes.fr/cea-00819299

T. Hain, H. Hossain, S. Chatterjee, S. Machata, U. Volk et al., Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e ??B regulon, BMC Microbiology, vol.8, issue.1, p.20, 2008.
DOI : 10.1186/1471-2180-8-20

H. Bierne, C. Sabet, N. Personnic, and P. Cossart, Internalins: a complex family of leucine-rich repeat-containing proteins in Listeria monocytogenes, Microbes and Infection, vol.9, issue.10, pp.1156-66, 2007.
DOI : 10.1016/j.micinf.2007.05.003

J. Vogel and K. Papenfort, Small non-coding RNAs and the bacterial outer membrane, Current Opinion in Microbiology, vol.9, issue.6, pp.605-616, 2006.
DOI : 10.1016/j.mib.2006.10.006

G. Klein and R. S. , Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs, BioMed Research International, vol.175, issue.15, p.153561, 2015.
DOI : 10.1074/jbc.m708163200

X. Deng, A. Phillippy, Z. Li, S. Salzberg, and W. Zhang, Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification, BMC Genomics, vol.11, issue.1, p.500, 2010.
DOI : 10.1186/1471-2164-11-500

A. Roberts, K. Nightingale, G. Jeffers, E. Fortes, J. Kongo et al., Genetic and phenotypic characterization of Listeria monocytogenes lineage III, Microbiology, vol.152, issue.3, pp.685-93, 2006.
DOI : 10.1099/mic.0.28503-0

H. Bakker, B. Bowen, L. Rodriguez-rivera, and M. Wiedmann, ABSTRACT, Applied and Environmental Microbiology, vol.78, issue.6, pp.1876-89, 2012.
DOI : 10.1128/AEM.06969-11

J. Dutheil and N. Galtier, Detecting groups of co-evolving positions in a molecule: a clustering approach, BMC Evolutionary Biology, vol.7, issue.1, p.242, 2007.
DOI : 10.1186/1471-2148-7-242

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos et al., BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009.
DOI : 10.1186/1471-2105-10-421

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-421?site=bmcbioinformatics.biomedcentral.com

J. Köster and S. Rahmann, Snakemake--a scalable bioinformatics workflow engine, Bioinformatics, vol.5, issue.11, pp.2520-2522, 2012.
DOI : 10.1186/1471-2105-5-40

D. Fouts, L. Brinkac, E. Beck, J. Inman, and G. Sutton, PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species, Nucleic Acids Research, vol.60, issue.22, p.172, 2012.
DOI : 10.1007/s00248-010-9692-8

C. Do, M. Mahabhashyam, M. Brudno, and S. Batzoglou, ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Research, vol.15, issue.2, pp.330-370, 2005.
DOI : 10.1101/gr.2821705

URL : http://genome.cshlp.org/content/15/2/330.full.pdf

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-52, 2000.
DOI : 10.1080/106351598261067

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

URL : http://doi.org/10.1371/journal.pone.0009490

J. Beaulieu, O. Meara, B. Donoghue, and M. , Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms, Systematic Biology, vol.141, issue.5, pp.725-762, 2013.
DOI : 10.1007/BF00160154

R. Fitzjohn, W. Maddison, and S. Otto, Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies, Systematic Biology, vol.4, issue.6, pp.595-611, 2009.
DOI : 10.1186/1471-2148-4-28

T. Kim and W. Hao, DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood, BMC Bioinformatics, vol.15, issue.1, p.320, 2014.
DOI : 10.1534/g3.113.009910

D. Yekutieli and Y. Benjamini, under dependency, The Annals of Statistics, vol.29, issue.4, pp.1165-88, 2001.
DOI : 10.1214/aos/1013699998

A. Wenzel, E. Akbasli, and J. Gorodkin, RIsearch: fast RNA???RNA interaction search using a simplified nearest-neighbor energy model, Bioinformatics, vol.35, issue.Database issue, pp.2738-2784, 2012.
DOI : 10.1093/nar/gkm487

A. Gruber, R. Lorenz, S. Bernhart, R. Neuböck, and I. Hofacker, The Vienna RNA Websuite, Nucleic Acids Research, vol.12, issue.10, pp.70-74, 2008.
DOI : 10.1101/gr.361602

A. Ropelewski, H. Nicholas, and D. Deerfield, Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch, Curr Protoc Bioinformatics, vol.17, 2004.
DOI : 10.1016/0097-8485(93)85006-X

P. Wright, G. J. Mann, M. Sorescu, D. Richter, A. Lott et al., CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains, Nucleic Acids Research, vol.40, issue.Database issue, pp.119-142, 2014.
DOI : 10.1093/nar/gks847

URL : https://academic.oup.com/nar/article-pdf/42/W1/W119/7438346/gku359.pdf

D. Womble, GCG: The Wisconsin Package of Sequence Analysis Programs, Methods Mol Biol, vol.132, pp.3-22, 2000.
DOI : 10.1385/1-59259-192-2:3

P. Kerpedjiev, S. Hammer, and I. Hofacker, Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams, Bioinformatics, vol.31, issue.20, pp.3377-3386, 2015.
DOI : 10.1109/TNB.2005.853646

URL : http://europepmc.org/articles/pmc4595900?pdf=render