G. Saddler, J. Bradbury, D. Brenner, N. Krieg, J. Staley et al., The Proteobacteria In Bergey's Manual of Systematic Bacteriology Edited by, p.63, 2005.

D. Meyer and A. Bogdanove, Genomics-driven advances in Xanthomonas biology In Plant Pathogenic Bacteria: Genomics and Molecular Biology Edited by: Jackson RW, pp.147-161

A. Simpson, F. Reinach, P. Arruda, F. Abreu, M. Acencio et al., The genome sequence of the plant pathogen Xylella fastidiosa, Nature, vol.406, pp.151-157, 2000.

X. Nesme, M. Vaneechoutte, S. Orso, B. Hoste, and J. Swings, Diversity and Genetic Relatedness within Genera Xanthomonas and Stenotrophomonas Using Restriction Endonuclease Site Differences of PCR-amplified 16S rRNA Gene, Systematic and Applied Microbiology, vol.18, issue.1, pp.127-135, 1995.
DOI : 10.1016/S0723-2020(11)80460-1

H. Lu, P. Patil, V. Sluys, M. White, F. Ryan et al., Acquisition and Evolution of Plant Pathogenesis???Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas, PLoS ONE, vol.5, issue.11, p.3828, 2008.
DOI : 10.1371/journal.pone.0003828.s004

A. Varani, W. De-lima, L. Moreira, M. De-oliveira, R. Souza et al., Common genes and genomic breaks: a detailed case study of the Xylella fastidiosa genome backbone and evolutionary insights, Plant Pathogenic Bacteria, pp.113-133

P. Rott, D. M. Rott, P. Bailey, R. Comstock, J. Croft et al., Leaf scald. In A guide to sugarcane diseases Edited by Montpellier: CIRAD-ISSCT; 2000:339. 8. Birch RG: Xanthomonas albilineans and the antipathogenesis approach to disease control, Mol Plant Pathol, vol.2, pp.1-11, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00729313

S. Hashimi, M. Wall, A. Smith, A. Maxwell, and R. Birch, The Phytotoxin Albicidin is a Novel Inhibitor of DNA Gyrase, Antimicrobial Agents and Chemotherapy, vol.51, issue.1, pp.181-187, 2007.
DOI : 10.1128/AAC.00918-06

R. Leite, . Jr, G. Minsavage, U. Bonas, and R. Stall, Detection and identification of phytopathogenic Xanthomonas strains by amplification of DNA sequences related to the hrp genes of Xanthomonas campestris pv. vesicatoria, Appl Environ Microbiol, vol.60, pp.1068-1077, 1994.

P. Champoiseau, J. Daugrois, I. Pieretti, S. Cociancich, M. Royer et al., , the Sugarcane Leaf Scald Pathogen, in Guadeloupe, Phytopathology, vol.96, issue.10, pp.1081-1091, 2006.
DOI : 10.1094/PHYTO-96-1081

H. Ochiai, Y. Inoue, M. Takeya, A. Sasaki, and H. Kaku, Genome Sequence of Xanthomonas oryzae pv. oryzae Suggests Contribution of Large Numbers of Effector Genes and Insertion Sequences to Its Race Diversity, Japan Agricultural Research Quarterly: JARQ, vol.39, issue.4, pp.275-287, 2005.
DOI : 10.6090/jarq.39.275

A. Da-silva, J. Ferro, F. Reinach, C. Farah, L. Furlan et al., Comparison of the genomes of two Xanthomonas pathogens with differing host specificities, Nature, vol.417, issue.6887, pp.459-463, 2002.
DOI : 10.1038/417459a

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, Journal of Bacteriology, vol.187, issue.21, pp.7254-7266, 2005.
DOI : 10.1128/JB.187.21.7254-7266.2005

L. Crossman, V. Gould, J. Dow, G. Vernikos, A. Okazaki et al., The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants, Genome Biology, vol.9, issue.4, p.74, 2008.
DOI : 10.1186/gb-2008-9-4-r74

S. Taghavi, C. Garafola, S. Monchy, L. Newman, A. Hoffman et al., Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees, Applied and Environmental Microbiology, vol.75, issue.3, pp.748-757, 2009.
DOI : 10.1128/AEM.02239-08

M. Van-sluys, D. Oliveira, M. Monteiro-vitorello, C. Miyaki, C. Furlan et al., Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa, Journal of Bacteriology, vol.185, issue.3, pp.1018-1026, 2003.
DOI : 10.1128/JB.185.3.1018-1026.2003

L. Li, C. Stoeckert, . Jr, and D. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003.
DOI : 10.1101/gr.1224503

Y. Wang, S. Zhao, and C. Hill, Rhs elements comprise three subfamilies which diverged prior to acquisition by Escherichia coli, J Bacteriol, vol.180, pp.4102-4110, 1998.

M. Royer, L. Costet, E. Vivien, M. Bes, A. Cousin et al., Is Encoded by Three Large PKS and NRPS Genes Present in a Gene Cluster Also Containing Several Putative Modifying, Regulatory, and Resistance Genes, Molecular Plant-Microbe Interactions, vol.17, issue.4, pp.414-427, 2004.
DOI : 10.1094/MPMI.2004.17.4.414

G. Cornelis, The type III secretion injectisome, Nature Reviews Microbiology, vol.103, issue.11, pp.811-825, 2006.
DOI : 10.1038/nrmicro1526

A. Boraston, D. Bolam, H. Gilbert, and G. Davies, Carbohydrate-binding modules: fine-tuning polysaccharide recognition, Biochemical Journal, vol.382, issue.3, pp.769-781, 2004.
DOI : 10.1042/BJ20040892

M. Howard, N. Ekborg, L. Taylor, S. Hutcheson, and R. Weiner, Identification and analysis of polyserine linker domains in www

M. Salanoubat, S. Genin, F. Artiguenave, J. Gouzy, S. Mangenot et al., Genome sequence of the plant pathogen Ralstonia solanacearum, Nature, vol.415, issue.6871, pp.497-502, 2002.
DOI : 10.1038/415497a

URL : https://hal.archives-ouvertes.fr/hal-00427300

T. Schiex, J. Gouzy, A. Moisan, D. Oliveira, and Y. , FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences, Nucleic Acids Research, vol.31, issue.13, pp.3738-3741, 2003.
DOI : 10.1093/nar/gkg610

A. Gattiker, K. Michoud, C. Rivoire, A. Auchincloss, E. Coudert et al., Automated annotation of microbial proteomes in SWISS-PROT, Computational Biology and Chemistry, vol.27, issue.1, pp.49-58, 2003.
DOI : 10.1016/S1476-9271(02)00094-4

M. Serres and M. Riley, K-12 Gene Products, Microbial & Comparative Genomics, vol.5, issue.4, pp.205-222, 2000.
DOI : 10.1089/omi.1.2000.5.205

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