J. Alfano and A. Collmer, The type III (Hrp) secretion pathway of plant pathogenic bacteria: trafficking harpins, Avr proteins, and death., Journal of Bacteriology, vol.179, issue.18, pp.5655-5662, 1997.
DOI : 10.1128/jb.179.18.5655-5662.1997

URL : http://jb.asm.org/content/179/18/5655.full.pdf

J. Alfano and A. Collmer, TYPE III SECRETION SYSTEM EFFECTOR PROTEINS: Double Agents in Bacterial Disease and Plant Defense, Annual Review of Phytopathology, vol.42, issue.1, pp.385-414, 2004.
DOI : 10.1146/annurev.phyto.42.040103.110731

A. Al-saadi, Homolog With 17.5 Repeats That Determines Pathogenicity on Citrus, but None Determine Host-Range Variation, Molecular Plant-Microbe Interactions, vol.20, issue.8, pp.934-943, 2007.
DOI : 10.1094/MPMI-20-8-0934

S. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf

. Anonymous, Council directive on protective measures against the introduction into the community of organisms harmful to plants or plant products and against their spread within the Community, Off. J. Eur. Communities, vol.29, issue.169, pp.1-112, 2000.

. Anonymous, EPPO standards PM 7/64. I. Diagnostics Xanthomonas arboricola pv. pruni, Bull. OEPP, vol.36, pp.129-133, 2006.

D. Arnold, R. Jackson, N. Waterfield, and J. Mansfield, Evolution of microbial virulence: the benefits of stress, Trends in Genetics, vol.23, issue.6, pp.293-300, 2007.
DOI : 10.1016/j.tig.2007.03.017

D. Barionovi and M. Scortichini, Assessment of integron gene cassette arrays in strains of Xanthomonas fragariae and X. arboricola pvs. fragariae and pruni, J. Plant Pathol, vol.88, pp.279-284, 2006.

D. Barionovi and M. Scortichini, strains, FEMS Microbiology Letters, vol.288, issue.1, pp.19-24, 2008.
DOI : 10.1111/j.1574-6968.2008.01315.x

P. Battilani, V. Rossi, and A. Saccardi, Development of Xanthomonas arboricola pv. pruni epidemics on peaches, J. Plant Pathol, vol.81, pp.161-171, 1999.

S. Boudon, C. Manceau, and J. Notteghem, Populations Causing Bacterial Spot of Stone Fruit Trees in Western Europe, Phytopathology, vol.95, issue.9, pp.1081-1088, 2005.
DOI : 10.1094/PHYTO-95-1081

D. Büttner and U. Bonas, virulence factors, FEMS Microbiology Reviews, vol.181, issue.2, pp.107-133, 2010.
DOI : 10.1046/j.1365-2958.2002.02964.x

G. Cirvilleri, Occurrence of Xanthomonas arboricola pv. corylina on hazelnut orchards in Sardinia and Sicily, J. Plant Pathol, vol.88, p.338, 2006.

A. Silva, Comparison of the genomes of two Xanthomonas pathogens with differing host specificities, Nature, vol.36, issue.6887, pp.459-463, 2002.
DOI : 10.1046/j.1365-2958.2000.01870.x

D. Kam and M. , The identification of the two subspecies of Xanthomonas populi in vitro, Forest Pathology, vol.31, issue.1-2, pp.25-29, 1981.
DOI : 10.1038/178703a0

D. Kam and M. , Xanthomonas campestris pv. populi, the causal agent of bark necrosis in poplar, Netherlands Journal of Plant Pathology, vol.12, issue.1, pp.13-22, 1984.
DOI : 10.1007/BF02014178

E. Fargier, M. Fischer-le-saux, and C. Manceau, A multilocus sequence analysis of Xanthomonas campestris reveals a complex structure within crucifer-attacking pathovars of this species, Systematic and Applied Microbiology, vol.34, issue.2, pp.156-165, 2011.
DOI : 10.1016/j.syapm.2010.09.001

M. Gillings, M. Holley, H. Stokes, and A. Holmes, Integrons in Xanthomonas: A source of species genome diversity, Proc. Natl. Acad. Sci, 2005.
DOI : 10.1093/nar/gki206

URL : http://www.pnas.org/content/102/12/4419.full.pdf

U. S. , , pp.4419-4424

S. Grant, E. Fisher, J. Chang, B. Mole, and J. Dangl, Subterfuge and Manipulation: Type III Effector Proteins of Phytopathogenic Bacteria, Annual Review of Microbiology, vol.60, issue.1, pp.425-449, 2006.
DOI : 10.1146/annurev.micro.60.080805.142251

J. Greenberg and B. Vinatzer, Identifying type III effectors of plant pathogens and analyzing their interaction with plant cells, Current Opinion in Microbiology, vol.6, issue.1, pp.20-28, 2003.
DOI : 10.1016/S1369-5274(02)00004-8

A. Guidot, Genomic Structure and Phylogeny of the Plant Pathogen Ralstonia solanacearum Inferred from Gene Distribution Analysis, Journal of Bacteriology, vol.189, issue.2, pp.377-387, 2007.
DOI : 10.1128/JB.00999-06

URL : http://jb.asm.org/content/189/2/377.full.pdf

D. Gürlebeck, F. Thieme, and U. Bonas, Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant, Journal of Plant Physiology, vol.163, issue.3, pp.233-255, 2006.
DOI : 10.1016/j.jplph.2005.11.011

A. Hajri, A ??Repertoire for Repertoire?? Hypothesis: Repertoires of Type Three Effectors are Candidate Determinants of Host Specificity in Xanthomonas, PLoS ONE, vol.132, issue.4, p.6632, 2009.
DOI : 10.1371/journal.pone.0006632.s002

URL : https://hal.archives-ouvertes.fr/hal-00729932

A. Hajri, Identification of a genetic lineage within Xanthomonas arboricola pv. juglandis as the causal agent of vertical oozing canker of Persian (English) walnut in France, Plant Pathology, vol.117, issue.6, pp.1014-1022, 2010.
DOI : 10.1099/00207713-52-2-573

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3059.2010.02362.x/pdf

A. Hajri, Multilocus sequence analysis and type three effector repertoires mining provide new insights into evolutionary history and virulence of Xanthomonas oryzae, Mol. Plant Pathol, 2011.

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

J. Janse, Bacterial leaf blight of strawberry (Fragaria (x) ananassa) caused by a pathovar of Xanthomonas arboricola, not similar to Xanthomonas fragariae Kennedy & King. Description of the causal organism as Xanthomonas arboricola pv. fragariae (pv. nov., comb. nov.), Plant Pathology, vol.5, issue.6, pp.653-665, 2001.
DOI : 10.1016/S0723-2020(11)80250-X

J. Janse, Diagnostic methods for phytopathogenic bacteria of stone fruits and nuts in COST 873, EPPO Bulletin, vol.10, issue.Suppl. 3, pp.68-85, 2010.
DOI : 10.1111/j.1365-2672.1994.tb03064.x

J. Kimbrel, S. Givan, T. Temple, K. Johnson, and J. Chang, , 2011.

, Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics, Mol. Plant Pathol, vol.12, pp.580-594

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1038/scientificamerican1179-98

B. Kvitko, Deletions in the Repertoire of Pseudomonas syringae pv. tomato DC3000 Type III Secretion Effector Genes Reveal Functional Overlap among Effectors, PLoS Pathogens, vol.145, issue.4, p.1000388, 2009.
DOI : 10.1371/journal.ppat.1000388.s003

M. Lavie, B. Seunes, P. Prior, and C. Boucher, Strains, Molecular Plant-Microbe Interactions, vol.17, issue.8, pp.931-940, 2004.
DOI : 10.1094/MPMI.2004.17.8.931

B. Lee, The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice, Nucleic Acids Research, vol.33, issue.2, pp.577-586, 2005.
DOI : 10.1093/nar/gki206

C. Leslie, S. Uratsu, G. Mcgranahan, and A. Dandekar, Walnut (Juglans), Methods Mol. Biol, vol.344, pp.297-307, 2006.

M. Lindeberg, Molecular Plant-Microbe Interactions, vol.18, issue.4, pp.275-282, 2005.
DOI : 10.1094/MPMI-18-0275

S. Loreti, A. Gallelli, A. Belisario, E. Wajnberg, and L. Corazza, Investigation of genomic variability of Xanthomonas arboricola pv. juglandis by AFLP analysis, European Journal of Plant Pathology, vol.107, issue.6, pp.583-591, 2001.
DOI : 10.1023/A:1017951406237

W. Ma, F. Dong, J. Stavrinides, and D. Guttman, Type III Effector Diversification via Both Pathoadaptation and Horizontal Transfer in Response to a Coevolutionary Arms Race, PLoS Genetics, vol.71, issue.12, p.209, 2006.
DOI : 10.1371/journal.pgen.0020209.st002

N. Mhedbi-hajri, Sensing and adhesion are adaptive functions in the plant pathogenic xanthomonads, BMC Evolutionary Biology, vol.13, issue.5, p.67, 2011.
DOI : 10.1093/oxfordjournals.molbev.a004148

L. Moreira, 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, issue.1, p.238, 2010.
DOI : 10.1186/1471-2164-11-238

X. Nesme, Phytopathology, vol.84, issue.1, pp.101-107, 1994.
DOI : 10.1094/Phyto-84-101

Z. Nimchuk, E. Fisher, D. Desvaux, J. Chang, and J. Dangl, Type III Effectors Require a Catalytic Triad and a Novel N-Terminal Domain for Function, Molecular Plant-Microbe Interactions, vol.20, issue.4, pp.346-357, 2007.
DOI : 10.1094/MPMI-20-4-0346

L. Noël, F. Thieme, D. Nennstiel, and U. Bonas, cDNA-AFLP analysis unravels a genome-wide hrpG-regulon in the plant pathogen Xanthomonas campestris pv. vesicatoria, Molecular Microbiology, vol.6, issue.6, pp.1271-1281, 2001.
DOI : 10.1128/JB.182.7.1844-1853.2000

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

H. Ochman and N. Moran, Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, issue.5519, pp.1096-1099, 2001.
DOI : 10.1126/science.1058543

N. Palleroni, D. Hildebrand, M. Schroth, and M. Hendson, species and pathovars, Journal of Applied Bacteriology, vol.40, issue.5, pp.441-446, 1993.
DOI : 10.1094/Phyto-79-793

N. Parkinson, C. Cowie, J. Heeney, and D. Stead, Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.41, issue.1, pp.264-274, 2009.
DOI : 10.1099/00207713-41-1-172

I. Pieretti, The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae, BMC Genomics, vol.10, issue.1, p.616, 2009.
DOI : 10.1186/1471-2164-10-616

URL : https://hal.archives-ouvertes.fr/hal-00730091

A. Pitman, Exposure to Host Resistance Mechanisms Drives Evolution of Bacterial Virulence in Plants, Current Biology, vol.15, issue.24, pp.2230-2235, 2005.
DOI : 10.1016/j.cub.2005.10.074

J. Pothier, on apricot and plum in Switzerland, Plant Pathology, vol.70, issue.2, p.404, 2010.
DOI : 10.1111/j.1365-3059.2009.02247.x

N. Potnis, Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper, BMC Genomics, vol.20, issue.1, p.146, 2011.
DOI : 10.1094/MPMI-20-10-1250

W. Qian, Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris, Genome Research, vol.15, issue.6, 2005.
DOI : 10.1101/gr.3378705

, Genome Res, vol.15, pp.757-767

J. Rademaker, Comparison of AFLP and rep-PCR genomic fingerprinting with DNA--DNA homology studies: Xanthomonas as a model system, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.50, issue.2, pp.665-677, 2000.
DOI : 10.1099/00207713-50-2-665

J. Rademaker, Phytopathology, vol.95, issue.9, pp.1098-1111, 2005.
DOI : 10.1094/PHYTO-95-1098

L. Rohmer, D. Guttman, and J. Dangl, Diverse Evolutionary Mechanisms Shape the Type III Effector Virulence Factor Repertoire in the Plant Pathogen Pseudomonas syringae, Genetics, vol.167, issue.3, pp.1341-1360, 2004.
DOI : 10.1534/genetics.103.019638

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, pp.406-425, 1987.

S. Salzberg, Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A, BMC Genomics, vol.9, issue.1, p.204, 2008.
DOI : 10.1186/1471-2164-9-204

S. Sarkar, J. Gordon, G. Martin, and D. Guttman, Comparative Genomics of Host-Specific Virulence in Pseudomonas syringae, Genetics, vol.174, issue.2, pp.1041-1056, 2006.
DOI : 10.1534/genetics.106.060996

L. Schechter, DC3000 Type III Secretion System Effector Proteins, Molecular Plant-Microbe Interactions, vol.19, issue.11, pp.1180-1192, 2006.
DOI : 10.1094/MPMI-19-1180

M. Scortichini, U. Marchesi, D. Prospero, and P. , Genetic Diversity of Xanthomonas arboricola pv. juglandis (synonyms: X. campestris pv. juglandis; X. juglandis pv. juglandis) Strains from Different Geographical Areas shown by Repetitive Polymerase Chain Reaction Genomic Fingerprinting, Journal of Phytopathology, vol.149, issue.6, pp.325-332, 2001.
DOI : 10.1046/j.1439-0434.2001.00628.x

M. Scortichini, M. Rossi, and U. Marchesi, Genetic, phenotypic and pathogenic diversity of Xanthomonas arboricola pv. corylina strains question the representative nature of the type strain, Plant Pathology, vol.81, issue.3, pp.374-381, 2002.
DOI : 10.1099/00207713-45-3-472

M. Scortichini and M. Rossi, Genetic Diversity of Xanthomonas arboricola pv. fragariae Strains and Comparison with some other X. arboricola Pathovars using Repetitive PCR Genomic Fingerprinting, Journal of Phytopathology, vol.151, issue.3, pp.113-119, 2003.
DOI : 10.1046/j.1439-0434.2003.00591.x

E. Sokurenko, D. Hasty, and D. Dykhuizen, Pathoadaptive mutations: gene loss and variation in bacterial pathogens, Trends in Microbiology, vol.7, issue.5, pp.191-195, 1999.
DOI : 10.1016/S0966-842X(99)01493-6

R. Staden, K. Beal, and J. Bonfield, The Staden Package, Methods Mol. Biol, vol.132, pp.115-130, 2000.
DOI : 10.1385/1-59259-192-2:115

J. Stavrinides, H. Mccann, and D. Guttman, Host???pathogen interplay and the evolution of bacterial effectors, Cellular Microbiology, vol.62, issue.0, pp.285-292, 2008.
DOI : 10.1128/JB.188.4.1405-1410.2006

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2007.01078.x/pdf

C. Stevens, M. Bennett, E. Athanassopoulos, G. Tsiamis, J. Taylor et al., Sequence variations in alleles of the avirulence gene avrPphE.R2 from Pseudomonas syringae pv. phaseolicola lead to loss of recognition of the AvrPphE protein within bean cells and a gain in cultivar-specific virulence, Molecular Microbiology, vol.29, issue.1, pp.165-177, 1998.
DOI : 10.1094/MPMI-9-0105

, Genetic Determinants of X. arboricola Pathogenicity, 2012.

D. Studholme, Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas???wilt, FEMS Microbiology Letters, vol.18, issue.2, pp.182-192, 2010.
DOI : 10.1080/00288233.1978.10427397

S. Swarup, D. Feyter, R. Brlansky, R. Gabriel, and D. , to Elicit Cankerlike Lesions on Citrus, Phytopathology, vol.81, issue.7, pp.802-809, 1991.
DOI : 10.1094/Phyto-81-802

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092

F. Thieme, 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

F. Thieme, Trigger Plant Reactions Dependent on a Conserved N-Myristoylation Motif, Molecular Plant-Microbe Interactions, vol.20, issue.10, pp.1250-1261, 2007.
DOI : 10.1094/MPMI-20-10-1250

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

L. Vauterin, B. Hoste, K. Kersters, and J. Swings, Reclassification of Xanthomonas, International Journal of Systematic Bacteriology, vol.45, issue.3, pp.472-489, 1995.
DOI : 10.1099/00207713-45-3-472

F. Vorhölter, The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis, Journal of Biotechnology, vol.134, issue.1-2, pp.33-45, 2008.
DOI : 10.1016/j.jbiotec.2007.12.013

F. White, N. Potnis, J. Jones, and R. Koebnik, Molecular Plant Pathology, vol.11, issue.1, pp.749-766, 2009.
DOI : 10.1094/MPMI-8-0627

J. Young, D. Park, H. Shearman, and E. Fargier, A multilocus sequence analysis of the genus Xanthomonas, Systematic and Applied Microbiology, vol.31, issue.5, pp.366-377, 2008.
DOI : 10.1016/j.syapm.2008.06.004

M. Zaccardelli, P. Ceroni, and U. Mazzucchi, Amplified fragment length polymorphism fingerprinting of Xanthomonas arboricola pv. pruni, J. Plant Pathol, vol.81, pp.173-179, 1999.