, Xcv 85-10), X. campestris pv. musacearum strain NCPPB4381 (Xcm NCPPB4381), X. oryzae pv. oryzae strain PXO99A (Xoo PXO99A), X. oryzae pv. oryzicola strain BLS256 (Xoc BLS256), X. gardneri strain ATCC19865 (Xg ATCC19865), X. vesicatoria strain ATCC35937 (Xv ATCC35937), X. campestris pv. campestris strain ATCC33913 (Xcc ATCC33913), X. campestris pv. raphani strain 756C (Xcr 756C), pp.85-95

, Bold line indicates that bootstrap value (1000 replicates) is 100, if not, bootstrap value of the branch is indicated on the tree

, 5 CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France. 6 CEA, Genoscope, Centre National de Séquençage, F-91057, Angers, France. 3 Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, F-49045, Angers, France. 4 INRA, LIPM UMR 441, F-31326, vol.277, pp.1-119, 10003.

L. Vauterin, J. Rademaker, and J. Swings, Synopsis on the taxonomy of the genus Xanthomonas, vol.90, pp.677-682, 2000.

L. Vauterin, B. Hoste, K. Kersters, and J. Swings, Reclassification of Xanthomonas, Int J Syst Bacteriol, vol.45, pp.472-489, 1995.

D. W. Dye, J. F. Bradbury, M. Goto, A. C. Hayward, R. A. Lelliott et al., International standards for naming pathovars of phytopathogenic and a list of pathovar names and pathotype strains, Rev Plant Pathol, vol.59, pp.153-168, 1980.

W. J. Broughton, G. Hern, M. Blair, S. Beebe, P. Gepts et al., Beans (Phaseolus spp.) -model food legumes, Plant Soil, vol.252, pp.55-128, 2003.

A. K. Vidaver, Xanthomonas campestris pv. phaseoli: cause of common bacterial blight of bean, Xanthomonas, pp.40-44, 1993.

P. H. Graham and C. P. Vance, Update on legume utilization legumes: importance and constraints to greater Use, Plant Physiol, vol.131, pp.872-877, 2003.

L. Kaplan and T. F. Lynch, Phaseolus ( fabaceae ) in archaeology: AMS, Econ Bot, vol.53, pp.261-272, 1999.

P. Gepts, Origin and evolution of common bean: past events and recent trends, Hortscience, vol.33, pp.1124-1130, 1998.

S. P. Singh and C. G. Munoz, Resistance to common bacterial blight among phaseolus species and common bean improvement, Crop Sci, vol.39, pp.80-89, 1999.

P. N. Miklas, J. D. Kelly, S. E. Beebe, and M. W. Blair, Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding, Euphytica, vol.147, pp.105-131, 2006.

D. M. Weller and A. W. Saettler, Colonization and distribution of Xanthomonas phaseoli and Xanthomonas phaseoli var. fuscans in field-grown navy beans, Phytopathology, vol.70, pp.500-506, 1980.

M. Jacques, J. K. Darrasse, A. Samson, and R. , Xanthomonas axonopodis pv. Phaseoli var. Fuscans Is aggregated in stable Biofilm population sizes in the phyllosphere of Field-grown beans, vol.71, pp.2008-2015, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01134886

A. Darrasse, C. Bureau, R. Samson, C. Morris, and M. Jacques, Contamination of bean seeds by Xanthomonas axonopodis pv. phaseoli associated with low bacterial densities in the phyllosphere under field and greenhouse conditions, Eur J Plant Pathol, vol.119, pp.203-215, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02667773

D. Büttner and U. Bonas, Regulation and secretion of Xanthomonas virulence factors, FEMS Microbiol Rev, vol.34, pp.107-133, 2010.

A. Darsonval, A. Darrasse, K. Durand, C. Bureau, S. Cesbron et al., Adhesion and fitness in the bean phyllosphere and transmission to seed of Xanthomonas fuscans subsp. fuscans, Mol Plant Microbe Interact, vol.22, pp.747-757, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02660257

A. Darsonval, A. Darrasse, D. Meyer, M. Demarty, K. Durand et al., Type III secretion system of Xanthomonas fuscans subsp. fuscans is involved in the phyllosphere colonization process and in transmission to seeds of susceptible beans, Appl Environ Microbiol, vol.74, pp.2669-2678, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02656610

A. Hajri, C. Brin, G. Hunault, F. Lardeux, C. Lemaire et al., A « repertoire for repertoire » hypothesis : repertoires of type three effectors are candidate determinants of host specificity in xanthomonas, PLoS One, vol.4, issue.8, p.6632, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00729932

P. H. Goodwin and C. R. Sopher, Water stress in leaves of Phaseolus vulgaris infected with Xanthomonas campestris pv. phaseoli, J Phytopathol, vol.140, pp.219-226, 1994.

P. Birch, L. J. Hyman, R. Taylor, A. F. Opio, C. Bragard et al., RAPD PCR-based differentiation of Xanthomonas campestris pv. phaseoli and Xanthomonas campestris pv. phaseoli var. fuscans, Eur J Plant Pathol, vol.103, pp.809-814, 1997.

I. K. Toth, L. J. Hyman, R. Taylor, and P. Birch, PCR-based detection of Xanthomonas campestris pv. phaseoli var. fuscans in plant material and its differentiation from X. c. pv. phaseoli, J Appl Microbiol, vol.85, pp.327-336, 1998.

D. Fourie, Distribution and severity of bacterial diseases on Dry beans (phaseolus vulgaris L.) in south africa, J Phytopathol, vol.150, pp.220-226, 2002.

R. I. Gilbertson, M. M. Otoya, M. A. Pastor-corrales, and D. P. Maxwell, Genetic diversity in common blight bacteria is revealed by cloned repetitive DNA sequences. Annual Report of the Bean Improvement Cooperative, vol.34, pp.37-38, 1991.

A. Mkandawire, R. B. Mabagala, P. Guzman, P. Gepts, and R. L. Gilbertson, Genetic diversity and pathogenic variation of common blight bacteria (Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans) suggests pathogen coevolution with the common bean, Phytopathology, vol.94, pp.593-603, 2004.

S. M. Alavi, S. Sanjari, F. Durand, C. Brin, C. Manceau et al., Assessment of the genetic diversity of Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans as a basis to identify putative pathogenicity genes and a type III secretion system of the SPI-1 family by multiple suppression subtractive hybridizations, Appl Environ Microbiol, vol.74, pp.3295-3301, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00729841

N. Mhedbi-hajri, A. Hajri, T. Boureau, A. Darrasse, K. Durand et al., Evolutionary history of the plant pathogenic bacterium xanthomonas axonopodis, vol.8, p.58474, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01199308

J. Rademaker, F. J. Louws, M. H. Schultz, U. Rossbach, L. Vauterin et al., A comprehensive species to strain taxonomic framework for Xanthomonas, Phytopathology, vol.95, pp.1098-1111, 2005.

C. T. Bull, S. H. De-boer, T. P. Denny, G. Firrao, -. Fischer et al., List of New names of plant pathogenic bacteria, vol.94, pp.21-27, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01209934

W. H. Burkholder, The bacterial diseases of bean: a comparative study, Ithaca. N. Y: Agric. Exp. Stn, p.88, 1930.

R. P. Ryan, F. Vorhölter, N. Potnis, J. B. Jones, M. Van-sluys et al., Pathogenomics of Xanthomonas: understanding bacteriumplant interactions, vol.9, pp.344-355, 2011.

D. Chinchilla, Z. Bauer, M. Regenass, T. Boller, and G. Felix, The arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception, Plant Cell, vol.18, pp.465-476, 2006.

P. R. Oblessuc, A. Borges, B. Chowdhury, D. Caldas, S. M. Tsai et al., Dissecting Phaseolus vulgaris innate immune system against Colletotrichum lindemuthianum infection, PLoS One, vol.7, p.43161, 2012.

G. S. Saddler and J. F. Bradbury, Family I . Xanthomonadaceae fam. nov. In Bergey's Manual of Systematic Bacteriology, vol.2, p.63, 2005.

I. Pieretti, M. Royer, V. Barbe, S. Carrere, R. Koebnik et al., The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae, BMC Genomics, vol.10, p.616, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00730091

M. Riley, Functions of the gene products of Escherichia coli, Microbiol Rev, vol.57, pp.862-952, 1993.

H. Tettlin, V. Masignani, M. J. Cieslewicz, C. Donati, D. Medini et al., Genome analysis of multiple pathogenic isolates of streptococcus agalactiae: implications for the microbial " pan-genome, Proc Natl Acad Sci U S A, vol.102, pp.13950-13955, 2005.

Y. Zhao, J. Wu, J. Yang, S. Sun, J. Xiao et al., PGAP : pan-genomes analysis pipeline, Bioinformatics, vol.28, pp.416-418, 2012.

H. Lu, P. Patil, V. Sluys, M. White, F. F. Ryan et al., Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in Xanthomonas, PLoS One, vol.3, p.3828, 2008.

A. J. Bogdanove, R. Koebnik, H. Lu, A. Furutani, S. V. Angiuoli et al., Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp, J Bacteriol, vol.193, pp.5450-5464, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02650254

J. M. Young, D. C. Park, H. Shearman, and E. Fargier, A multilocus sequence analysis of the genus Xanthomonas, Syst Appl Microbiol, vol.31, pp.366-377, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02663461

N. Jalan, V. Aritua, D. Kumar, F. Yu, J. B. Jones et al., Comparative genomic analysis of xanthomonas axonopodis pv. Citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity, J Bacteriol, vol.193, issue.22, pp.6342-6357, 2011.

A. Da-silva, J. A. Ferro, F. C. Reinach, C. S. Farah, L. R. Furlan et al., Comparison of the genomes of two Xanthomonas pathogens with differing host specificities, Nature, vol.417, pp.459-463, 2002.

D. Studholme, E. Kemen, D. Maclean, S. Schornack, V. Aritua et al., Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt, FEMS Microbiol Lett, vol.310, issue.2, pp.182-192, 2010.

F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch et al., Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence, J Bacteriol, vol.187, issue.21, pp.7254-7266, 2005.

L. M. Moreira, N. F. Almeida, N. Potnis, L. A. Diqanpietri, S. S. Adi et al., Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii, BMC Genomics, vol.11, p.238, 2010.

N. Potnis, K. Krasileva, V. Chow, N. F. Almeida, P. B. Patil et al., Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper, BMC Genomics, vol.12, p.146, 2011.

S. L. Salzberg, D. D. Sommer, M. C. Schatz, A. M. Phillippy, P. D. Rabinowicz et al., Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A, BMC Genomics, vol.9, p.204, 2008.

M. A. Van-sluys, M. C. De-oliveira, C. B. Monteiro-vitorello, C. Y. Miyaki, L. R. Furlan et al., Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa, J Bacteriol, vol.185, issue.3, pp.1018-1026, 2003.

O. Lukjancenko, D. W. Ussery, and T. M. Wassenaar, Comparative genomics of bifidobacterium, lactobacillus and related probiotic genera, Microb Ecol, vol.63, pp.651-673, 2012.

J. Bannantine, C. Wu, C. Hsu, S. Zhou, D. C. Schwartz et al., Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association, BMC Genomics, vol.13, p.89, 2012.

D. Baltrus, M. T. Nishimura, A. Romanchuk, J. H. Chang, M. S. Mukhtar et al., Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates, PLoS Pathog, vol.7, p.1002132, 2011.

D. Meyer and A. J. Bogdanove, Genomics-driven advances in Xanthomonas biology, Plant Pathogenic Bacteria: Genomics and Molecular Biology, pp.147-161, 2009.

B. Guieysse and S. Wuertz, Metabolically versatile large-genome prokaryotes, Curr Opin Biotechnol, vol.23, pp.1-7, 2011.

G. A. Beattie and S. E. Lindow, The secret life of foliar bacterial pathogens on leaves, Annu Rev Phytopathol, vol.33, pp.145-172, 1995.

I. Pieretti, M. Royer, V. Barbe, S. Carrere, R. Koebnik et al., Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels, BMC Genomics, vol.13, p.658, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01199327

M. Y. Galperin, Bacterial signal transduction network in a genomic perspective, Environ Microbiol, vol.6, pp.552-567, 2004.

M. Y. Galperin, A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts, BMC Microbiol, vol.5, p.35, 2005.

W. Qian, Z. Han, and C. He, Two-component signal transduction systems of xanthomonas spp.: a lesson from genomics, vol.21, pp.151-161, 2008.

M. Y. Galperin and E. V. Koonin, From complete genome sequence to ' complete ' understanding ?, Trends Biotechnol, vol.28, pp.398-406, 2010.

D. Kim and S. Forst, Genomic analysis of the histidine kinase family in bacteria and archaea, Microbiology, vol.147, pp.1197-1212, 2001.

L. Craig and J. Li, Type IV pili: paradoxes in form and function, Curr Opin Struc Biol, vol.18, pp.267-277, 2008.

L. L. Burrows, Pseudomonas aeruginosa twitching motility: type IV pili in action, Annu Rev Microbiol, vol.66, pp.493-520, 2012.

K. V. Korotkov, M. Sandkvist, and W. Hol, The type II secretion system: biogenesis, molecular architecture and mechanism, Nat Rev Microbiol, vol.10, pp.336-351, 2012.

Y. Meng, Y. Li, C. D. Galvani, G. Hao, J. N. Turner et al., Upstream migration of Xylella fastidiosa via pilus-driven twitching motility, J Bacteriol, vol.187, pp.5560-5567, 2005.

S. M. Lim, B. So, J. Wang, E. S. Song, Y. Park et al., Functional analysis of pilQ gene in Xanthomanas oryzae pv. oryzae, bacterial blight pathogen of rice, J Microbiol, vol.46, pp.214-220, 2008.

G. Waksman and S. J. Hultgren, Structural biology of the chaperone-usher pathway of pilus biogenesis, Nat Rev Micro, vol.7, pp.765-774, 2009.

M. Desvaux, M. Hébraud, R. Talon, and I. R. Henderson, Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria, Trends Microbiol, vol.17, pp.338-340, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02663736

N. Dautin and H. D. Bernstein, Protein secretion in gram-negative bacteria via the autotransporter pathway, Annu Rev Microbiol, vol.61, pp.89-112, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02539931

S. E. Cotter, N. K. Surana, and J. W. St-geme, Trimeric autotransporters: a distinct subfamily of autotransporter proteins, Trends Microbiol, vol.13, pp.199-205, 2005.

D. Linke, T. Riess, I. B. Autenrieth, A. Lupas, and V. Kempf, Trimeric autotransporter adhesins: variable structure, common function, Trends Microbiol, vol.14, pp.264-270, 2006.

J. Mazar and P. A. Cotter, Topology and maturation of filamentous haemagglutinin suggest a new model for two-partner secretion, Mol Microbiol, vol.62, pp.641-654, 2006.

N. Mhedbi-hajri, A. Darrasse, S. Pigné, K. Durand, S. Fouteau et al., Sensing and adhesion are adaptive functions in the plant pathogenic xanthomonads, BMC Evol Biol, vol.11, p.67, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02649867

I. Sutherland and . Xanthan, Xanthomonas, pp.363-388, 1993.

F. García-ochoa, V. E. Santos, J. A. Casas, and E. Gómez, Xanthan gum: production, recovery, and properties, Biotechnol Adv, vol.18, pp.549-579, 2000.

B. Vu, J. C. Russel, and E. P. Ivanova, Bacterial extracellular polysaccharides involved in biofilm formation, Molecules, vol.14, pp.2535-2554, 2009.

F. E. El-banoby and K. Rudolph, Multiplication of Xanthomonas campestris pvs secalis and translucens in host and non-host plants (rye and barley) and development of water soaking, EPPO Bull, vol.19, pp.105-111, 1989.

P. Vidhyasekaran, M. E. Alvenda, and T. W. Mew, Physiological changes in rice seedlings induced by extracellular polysaccharide produced by Xanthomonas campestris pv. oryzae, Physiol Mol Plant Pathol, vol.35, pp.391-402, 1989.

G. Dunger, V. M. Relling, M. L. Tondo, M. Barreras, L. Ielpi et al., Xanthan is not essential for pathogenicity in citrus canker but contributes to Xanthomonas epiphytic survival, Arch Microbiol, vol.188, pp.127-135, 2007.

L. A. Rigano, F. Siciliano, E. R. Sendín, L. Filippone, P. Torres et al., Biofilm formation, epiphytic fitness, and canker development in xanthomonas axonopodis pv. Citri, Mol Plant Microbe Interact, vol.20, pp.1222-1230, 2007.

F. Vorhölter, S. Schneiker, A. Goesmann, L. Krause, T. Bekel et al., The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis, J Biotech, vol.134, pp.33-45, 2008.

K. Yoon and J. Cho, Transcriptional analysis of the gum gene cluster from Xanthomonas oryzae pathovar oryzae, Biotechnol Lett, vol.29, pp.95-103, 2007.

R. Köplin, W. Arnold, B. Hotte, R. Simon, G. E. Wang et al., Genetics of xanthan production in xanthomonas campestris: the xanA and xanB genes Are involved in UDP-glucose and GDP-mannose biosynthesis, J Bacteriol, vol.174, pp.191-199, 1992.

F. Tao, S. Swarup, L. , Z. Biology, and C. , Quorum sensing modulation of a putative glycosyltransferase gene cluster essential for Xanthomonas campestris biofilm formation, Environ Microbiol, vol.12, pp.3159-3170, 2010.

X. Wang, J. Iii, and T. Romeo, The pgaABCD locus of escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation, J Appl Microbiol, vol.186, pp.2724-2734, 2004.

A. G. Bobrov, O. Kirillina, S. Forman, D. Mack, and R. D. Perry, Insights into Yersinia pestis biofilm development: topology and co-interaction of Hms inner membrane proteins involved in exopolysaccharide production, Environ Microbiol, vol.10, pp.1419-1432, 2008.

C. Raetz and C. Whitfield, Lipopolysaccharide endotoxins, Annu Rev Biochem, vol.71, pp.635-700, 2002.

P. Sperandeo, G. Dehò, and A. Polissi, The lipopolysaccharide transport system of gram-negative bacteria, Biochim Biophys Acta, vol.1791, pp.594-602, 2009.

D. Steinmann, R. Köplin, A. Pühler, and K. Niehaus, Xanthomonas campestris pv. Campestris lpsI and lpsJ genes encoding putative proteins with sequence similarity to the ?-and -subunits of 3-oxoacid CoA-transferases are involved in LPS biosynthesis, Arch Microbiol, vol.168, pp.441-447, 1997.

C. Raetz, C. M. Reynolds, M. S. Trent, and R. E. Bishop, Lipid a modification systems in gram-negative bacteria, Annu Rev Biochem, vol.76, pp.295-329, 2007.

P. B. Patil, A. J. Bogdanove, and R. V. Sonti, The role of horizontal transfer in the evolution of a highly variable lipopolysaccharide biosynthesis locus in xanthomonads that infect rice, citrus and crucifers, BMC Evol Biol, vol.7, p.243, 2007.

A. V. Perepelov, D. Li, B. Liu, S. N. Senchenkova, D. Guo et al., Structural and genetic characterization of O99 antigen, FEMS Immunol Med Microbiol, vol.57, pp.80-87, 2009.

H. Neugebauer, C. Herrmann, W. Kammer, G. Schwarz, A. Nordheim et al., ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of caulobacter crescentus, J Bacteriol, vol.187, pp.8300-8311, 2005.

S. Blanvillain, D. Meyer, A. Boulanger, M. Lautier, C. Guynet et al., Plant carbohydrate scavenging through TonBdependent receptors: a feature shared by phytopathogenic and aquatic bacteria, PLoS One, vol.2, issue.2, p.224, 2007.

S. Eisenbeis, S. Lohmiller, M. Valdebenito, S. Leicht, and V. Braun, NagA-dependent uptake of N-acetyl-glucosamine and N-acetyl-chitin oligosaccharides across the outer membrane of caulobacter crescentus, J Bacteriol, vol.190, pp.5230-5238, 2008.

K. Schauer, D. Rodionov, and H. De-reuse, New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'?, Trends Biochem Sci, vol.33, pp.330-338, 2008.

N. Noinaj, M. Guillier, T. J. Barnard, and S. K. Buchanan, TonB-dependent transporters: regulation, structure, and function, Annu Rev Microbiol, vol.64, pp.43-60, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00555668

A. Boulanger, G. Déjean, M. Lautier, M. Glories, C. Zischek et al., Identification and regulation of the N-acetylglucosamine utilization pathway of the plant pathogenic bacterium xanthomonas campestris pv. Campestris, J Bacteriol, vol.192, pp.1487-1497, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02658519

G. Déjean, S. Blanvillain-baufumé, A. Boulanger, A. Darrasse, T. D. De-bernonville et al., he xylan utilization system of the plant pathogen xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts, New Phytol, 2013.

R. P. Ryan and J. M. Dow, Intermolecular interactions between HD-GYP and GGDEF domain proteins mediate virulence-related signal transduction in Xanthomonas campestris, Virulence, vol.1, pp.404-408, 2010.

G. E. Gudesblat, P. S. Torres, and A. A. Vojnov, Xanthomonas campestris overcomes Arabidopsis stomatal innate immunity through a DSF cell-to-cell signal-regulated virulence factor, Plant Physiol, vol.149, pp.1017-1027, 2009.

U. Jenal and J. Malone, Mechanisms of cyclic-di-GMP signaling in bacteria, Annu Rev Genet, vol.40, pp.385-407, 2006.

R. P. Ryan, Y. Fouhy, J. F. Lucey, L. C. Crossman, S. Spiro et al., Cell-cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover, Proc Natl Acad Sci, vol.103, pp.6712-6717, 2006.

J. L. Tang, Y. N. Liu, C. E. Barber, J. M. Dow, J. C. Wootton et al., Genetic and molecular analysis of a cluster of rpf genes involved in positive regulation of synthesis of extracellular enzymes and polysaccharide in Xanthomonas campestris pathovar campestris, Mol Gen Genet, vol.226, pp.409-417, 1991.

S. Chatterjee, K. L. Newman, and S. E. Lindow, Cell-to-cell signaling in Xylella fastidiosa suppresses movement and xylem vessel colonization in grape, vol.21, pp.1309-1315, 2008.

K. S. Jeong, S. E. Lee, J. W. Han, S. U. Yang, B. M. Lee et al., Virulence reduction and differing regulation of virulence genes in rpf mutants of Xanthomonas oryzae pv. oryzae, Plant Pathol J, vol.24, pp.143-151, 2008.

A. R. Poplawsky and W. Chun, pigB determines a diffusible factor needed for extracellular polysaccharide slime and xanthomonadin production in Xanthomonas campestris pv. campestris, J Bacteriol, vol.179, pp.439-444, 1997.

Y. He, J. Wu, L. Zhou, F. Yang, Y. He et al., Xanthomonas campestris diffusible factor is 3-hydroxybenzoic acid and is associated with xanthomonadin biosynthesis, cell viability, antioxidant activity, and systemic invasion, Mol Plant Microbe Interact, vol.24, pp.948-957, 2011.

A. R. Poplawsky, D. M. Walters, P. E. Rouviere, and W. Chun, A gene for a dioxygenase-like protein determines the production of the DF signal in Xanthomonas campestris pv. campestris, Mol Plant Pathol, vol.6, pp.653-657, 2005.

A. K. Goel, L. Rajagopal, N. Nagesh, and R. V. Sonti, Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in xanthomonas oryzae pv, Oryzae. J Bacteriol, vol.184, pp.3539-3548, 2002.

L. Zhou, J. Wang, J. Wang, A. Poplawsky, S. Lin et al., The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways, Mol Microbiol, vol.87, pp.80-93, 2013.

D. Büttner, Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant-and animalpathogenic bacteria, Microbiol Mol Biol Rev, vol.76, pp.262-310, 2012.

, Delepelaire P: Type I secretion in gram-negative bacteria, Biochim Biophys Acta, vol.1694, pp.149-161, 2004.

M. Masi and C. Wandersman, Multiple signals direct the assembly and function of a type 1 secretion system, J Bacteriol, vol.192, pp.3861-3869, 2010.

J. Stavrinides, Origin and evolution of phytopathogenic bacteria, Plant Pathogenic Bacteria: Genomics and Molecular Biology, p.330, 2009.

M. Moreira, E. C. De-souza, and C. A. De-moraes, Multidrug efflux systems in gram-negative bacteria, Brazilian J Microbiol, vol.35, pp.19-28, 2004.

A. Burse, H. Weingart, and M. S. Ullrich, The phytoalexin-inducible multidrug efflux pump AcrAB contributes to virulence in the fire blight pathogen, Erwinia amylovora, Mol Plant Microbe Interact, vol.17, pp.43-54, 2004.

D. G. Brown, J. K. Swanson, and C. Allen, Two host-induced Ralstonia solanacearum genes, acrA and dinF, encode multidrug efflux pumps and contribute to bacterial wilt virulence, Appl Environ Microbiol, vol.73, pp.2777-2786, 2007.

J. D. Palumbo, C. I. Kado, and D. A. Phillips, An isoflavonoid-inducible efflux pump in agrobacterium tumefaciens is involved in competitive colonization of roots, J Bacteriol, vol.180, pp.3107-3113, 1998.

K. Poole, Bacterial Multidrug Efflux Pumps Serve Other Functions. Microbe, vol.3, pp.179-185, 2008.

T. Kuroda and T. Tsuchiya, Multidrug efflux transporters in the MATE family, Biochim Biophys Acta, vol.1794, pp.763-768, 2009.

E. Papanikou, S. Karamanou, and A. Economou, Bacterial protein secretion through the translocase nanomachine, Nat Rev Microbiol, vol.5, pp.839-851, 2007.

C. E. Alvarez-martinez and P. J. Christie, Biological diversity of prokaryotic type IV secretion systems, Microbiol Mol Biol Rev, vol.73, pp.775-808, 2009.

R. Fronzes, P. J. Christie, and G. Waksman, The structural biology of type IV secretion systems, Nat Rev Micro, vol.7, pp.703-714, 2009.

J. Guglielmini, F. De-la-cruz, and E. Rocha, Evolution of conjugation and type IV secretion systems, Mol Biol Evol, vol.30, pp.315-331, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01374951

M. C. Alegria, D. P. Souza, M. O. Andrade, C. Docena, L. Khater et al., Identification of New protein-protein interactions involving the products of the chromosome-and plasmid-encoded type IV secretion loci of the phytopathogen xanthomonas axonopodis pv. Citri, J Bacteriol, vol.187, pp.2315-2325, 2005.

D. P. Souza, M. O. Andrade, C. E. Alvarez-martinez, G. M. Arantes, S. Chuck et al., A component of the xanthomonadaceae type IV secretion system combines a VirB7 motif with a N0 domain found in outer membrane transport proteins, PLoS Pathog, vol.7, p.1002031, 2011.

M. Juhas, D. W. Crook, I. D. Dimopoulou, G. Lunter, R. M. Harding et al., Novel type IV secretion system involved in propagation of genomic islands, J Bacteriol, pp.761-771, 2007.

J. M. Silverman, Y. R. Brunet, E. Cascales, and J. D. Mougous, Structure and regulation of the type VI secretion system, Annu Rev Microbiol, vol.66, pp.453-472, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01458240

R. Szczesny, M. Jordan, C. Schramm, S. Schulz, V. Cogez et al., Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria, New Phytol, vol.187, pp.983-1002, 2010.

A. B. Boraston, D. N. Bolam, H. J. Gilbert, and G. J. Davies, Carbohydrate-binding modules: fine-tuning polysaccharide recognition, Biochem J, vol.382, pp.769-781, 2004.

J. Stavrinides, W. Ma, and D. S. Guttman, Terminal reassortment drives the quantum evolution of type III effectors in bacterial pathogens, PLoS Pathog, vol.2, p.104, 2006.

S. Fenselau and U. Bonas, Sequence and expression analysis of the hrpB pathogenicity operon of Xanthomonas campestris pv. campestris which encodes eight proteins with similarity to components of the Hrp, Ysc, Spa, and Fli secretion systems, Mol Plant Microbe Interact, vol.8, pp.845-854, 1995.

S. Cunac, C. Boucher, and S. Genin, Characterization of the cis-acting regulatory element controlling HrpB-mediated activation of the type III secretion system and effector genes in Ralstonia solanacearum, J Bacteriol, vol.186, pp.2309-2318, 2004.

R. Koebnik, A. Krüger, F. Thieme, A. Urban, and U. Bonas, Specific binding of the xanthomonas campestris pv. Vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoter boxes, J Bacteriol, vol.188, pp.7652-7660, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00163972

C. Schmidtke, S. Findeiss, C. M. Sharma, J. Kuhfuss, S. Hoffmann et al., Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions, Nucl Acids Res, vol.40, pp.2020-2031, 2012.

G. C. Palmer, P. A. Jorth, and M. Whiteley, The role of two Pseudomonas aeruginosa anthranilate synthases in tryptophan and quorum signal production, Microbiology, vol.159, pp.959-969, 2013.

S. M. Alavi, S. Poussier, and C. Manceau, Characterization of ISXax1, a novel insertion sequence restricted to Xanthomonas axonopodis pv. phaseoli (variants fuscans and non-fuscans) and Xanthomonas axonopodis pv. vesicatoria, Appl Environ Microbiol, vol.73, pp.1678-1682, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02668332

C. B. Monteiro-vitorello, M. C. De-oliveira, M. M. Zerillo, A. M. Varani, E. Civerolo et al., Xylella and Xanthomonas Mobil'omics, vol.9, pp.146-159, 2005.

J. Mahillon and M. Chandler, Insertion sequences, Microbiol Mol Biol Rev, vol.62, pp.725-774, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00021179

G. Shieh, C. Lin, J. Kuo, and T. Kuo, Characterization of an open reading frame involved in site-specific integration of filamentous phage Cf1t from xanthomonas campestris pv, Citri. Gene, vol.158, pp.73-76, 1995.

W. Qian, Y. Jia, S. X. Ren, Y. Q. He, J. X. Feng et al., Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris, Genome Res, vol.15, pp.757-767, 2005.

B. El-yacoubi, A. M. Brunings, Q. Yuan, S. Shankar, and D. W. Gabriel, In planta horizontal transfer of a major pathogenicity effector gene, Appl Environ Microbiol, vol.73, pp.1612-1621, 2007.

A. M. Brunnings and D. W. Gabriel, Xanthomonas citri: breaking the surface, Mol Plant Pathol, vol.4, pp.141-157, 2003.

R. Liu and H. Ochman, Stepwise formation of the bacterial flagellar system, Proc Natl Acad Sci U S A, vol.104, pp.7116-7121, 2007.

J. Swings, L. Vauterin, and K. Kersters, The bacterium Xanthomonas. In Xanthomonas, pp.121-156, 1993.

P. C. Ronald and B. Beutler, Plant and animal sensors of conserved microbial signatures, Science, vol.330, pp.1061-1064, 2010.

R. M. Macnab, How bacteria assemble flagella, Annu Rev Microbiol, vol.57, pp.77-100, 2003.

J. Yao and C. Allen, Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen ralstonia solanacearum, J Bacteriol, vol.188, pp.3697-3708, 2006.

S. H. Dzinic, M. Luercio, and J. L. Ram, Bacterial chemotaxis differences in Escherichia coli isolated from different hosts, Can J Plant Pathol, vol.54, pp.1043-1052, 2008.

L. Noël, F. Thieme, D. Nennstiel, and U. Bonas, Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island, J Bacteriol, vol.184, pp.1340-1348, 2002.

D. Hocquet, C. Llanes, M. Thouverez, H. D. Kulasekara, X. Bertrand et al., Evidence for induction of integron-based antibiotic resistance by the SOS response in a clinical setting, PLoS Pathog, vol.8, p.1002778, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00802793

M. R. Gillings, M. P. Holley, H. W. Stokes, and A. J. Holmes, Integrons in Xanthomonas: a source of species genome diversity, Proc Natl Acad Sci U S A, vol.102, pp.4419-4424, 2005.

C. Kuo and H. Ochman, The extinction dynamics of bacterial pseudogenes, PloS Genet, vol.6, p.1001050, 2010.

Y. Tutar and . Pseudogenes, Comp Funct Genomics, vol.2012, pp.6-9, 2012.

A. Carreira, L. M. Ferreira, and V. Loureiro, Brown pigments produced by yarrowia lipolytica result from extracellular accumulation of homogentisic acid, Appl Environ Microbiol, vol.67, pp.3463-3468, 2001.

D. R. Nemergut, M. S. Robeson, R. F. Kysela, A. P. Martin, S. K. Schmidt et al., Insights and inferences about integron evolution from genomic data, BMC Genomics, vol.9, p.261, 2008.

J. Aury, C. Cruaud, V. Barbe, O. Rogier, S. Mangenot et al., High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies, BMC Genomics, vol.9, p.603, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02659381

P. Thébaut, F. Servant, T. Schiex, and J. Gouzy, L'environnement iANT: integrated annotation tool, JOBIM Conference Proceedings: 3-5, pp.361-365, 2000.

T. Schiex, J. Gouzy, A. Moisan, and Y. De-oliveira, FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences, Nucl Acids Res, vol.31, pp.3738-3741, 2003.

A. Gattiker, K. Michoud, C. Rivoire, A. H. Auchincloss, E. Coudert et al., Automated annotation of microbial proteomes in SWISS-PROT, Comput Biol Chem, vol.27, pp.49-58, 2003.

M. H. Serres and M. Riley, MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products, Microb Comp Genomics, vol.5, pp.205-222, 2000.

L. Li, C. Stoeckert, and D. S. Roos, OrthoMCL : identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-2189, 2003.

A. E. Darling, B. Mau, and N. T. Perna, progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement, PLoS One, vol.5, p.11147, 2010.

T. A. Hall, BioEdit: a user-friendly biological sequence alignement editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp Ser, vol.41, pp.95-98, 1999.

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Sys Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, vol.28, pp.2731-2739, 2011.

. Darrasse, Submit your next manuscript to BioMed Central and take full advantage of: ? Convenient online submission ? Thorough peer review ? No space constraints or color figure charges ? Immediate publication on acceptance ? Inclusion in PubMed, CAS, Scopus and Google Scholar ? Research which is freely available for redistribution, BMC Genomics, vol.14, p.761, 2013.