J. R. Alfano and A. Collmer, Type III secretion system effector proteins: Double agents in bacterial disease and plant defense, Annual Review of. Phytopathology, vol.42, pp.385-414, 2004.

S. Andrews, FastQC: A quality control tool for high throughput sequence data, Bioinformatics, 2010.

C. Bartoli, J. R. Lamichhane, O. Berge, C. Guilbaud, and L. Varvaro,

G. M. Balestra, B. A. Vinatzer, and C. E. Morris, A framework to gauge the epidemic potential of plant pathogens in environmental reservoirs: the example of kiwifruit canker, Mol Plant Pathol, vol.16, pp.137-149, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02637074

O. Berge, C. L. Monteil, C. Bartoli, C. Chandeysson, C. Guilbaud et al., A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex, PLoS One, vol.9, 2014.

A. Block, T. Y. Toruño, C. G. Elowsky, C. Zhang, J. Steinbrenner et al., The Pseudomonas syringae type III effector HopD1 suppresses effector-triggered immunity, localizes to the endoplasmic reticulum, and targets the Arabidopsis transcription factor NTL9, New Phytol, vol.201, pp.1358-1370, 2014.

C. R. Buell, V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen et al., The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000, Proc Natl Acad Sci U S A, vol.100, pp.10181-10186, 2003.

R. Cai, J. Lewis, S. Yan, H. Liu, C. R. Clarke et al., The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity, Lindeberg, M. & other authors, vol.7, p.1002130, 2011.

R. Cai, S. Yan, H. Liu, S. Leman, and B. A. Vinatzer, Reconstructing host range evolution of bacterial plant pathogens using Pseudomonas syringae pv. tomato and its close relatives as a model, Infection Genetics and. Evolution, vol.11, pp.1738-1751, 2011.

T. Carver, N. Thomson, A. Bleasby, M. Berriman, and J. Parkhill, DNAPlotter: circular and linear interactive genome visualization, Bioinformatics, vol.25, pp.119-120, 2009.

X. M. Chen, Epidemiology and control of stripe rust Puccinia striiformis f. sp tritici on wheat, Canadian Journal of Plant Pathology, vol.27, pp.314-337, 2005.

L. Cheng, T. R. Connor, J. Siren, D. M. Aanensen, and J. Corander, Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software, Molecular Biology and. Evolution, vol.30, pp.1224-1228, 2013.

C. R. Clarke, D. J. Studholme, B. Hayes, B. Runde, A. Weisberg et al., Genome-enabled phylogeographic investigation of the quarantine pathogen Ralstonia solanacearum race 3 biovar 2 and screening for sources of resistance against its core effectors, Phytopathology, vol.105, pp.597-607, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02631393

H. A. Constantinidou, S. S. Hirano, L. S. Baker, and C. D. Upper, Atmospheric dispersal of ice nucleation-active bacteria: the role of rain, Phytopathology, vol.80, pp.934-937, 1990.

J. Corander, P. Waldmann, P. Marttinen, and M. J. Sillanpää, , 2004.

, BAPS 2: enhanced possibilities for the analysis of genetic population structure, Bioinformatics, vol.20, pp.2363-2369

J. Corander, P. Marttinen, J. Sirén, and J. Tang, Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinformatics, vol.9, 2008.

M. Demba-diallo, C. L. Monteil, B. A. Vinatzer, C. R. Clarke, C. Glaux et al., Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic, ISME J, vol.6, pp.1325-1335, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02646641

X. Didelot and D. Falush, Inference of bacterial microevolution using multilocus sequence data, Genetics, vol.175, pp.1251-1266, 2007.

H. Feil, W. S. Feil, P. Chain, F. Larimer, G. Dibartolo et al., Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000, Proc Natl Acad Sci U S A, vol.102, pp.11064-11069, 2005.

T. Garland, A. F. Bennett, and E. L. Rezende, Phylogenetic approaches in comparative physiology, J Exp Biol, vol.208, pp.3015-3035, 2005.

R. Gitaitis and R. Walcott, The epidemiology and management of seedborne bacterial diseases, Annu Rev Phytopathol, vol.45, pp.371-397, 2007.

M. V. Grosso-becerra, C. Santos-medellín, A. González-valdez, J. L. Méndez, G. Delgado et al., Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity, BMC Genomics, vol.15, 2014.

W. P. Hanage, C. Fraser, J. Tang, T. R. Connor, and J. Corander, , 2009.

, Hyper-recombination, diversity, and antibiotic resistance in pneumococcus, Science, vol.324, pp.1454-1457

D. R. Hann, A. Domínguez-ferreras, V. Motyka, P. I. Dobrev, S. Schornack et al., The Pseudomonas type III effector HopQ1 activates cytokinin signaling and interferes with plant innate immunity, New Phytol, vol.201, pp.585-598, 2014.

T. H. Hazen, P. C. Lafon, N. M. Garrett, T. M. Lowe, D. J. Silberger et al., Insights into the environmental reservoir of pathogenic Vibrio parahaemolyticus using comparative genomics, & other authors, vol.64, pp.624-653, 2000.

K. L. Hockett, M. Nishmura, E. Karsrud, and K. M. Dougherty,

D. A. Baltrus, P. syringae CC1557: a highly virulent strain with an unusually small type III effector repertoire that includes a novel effector, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02638544

V. Joardar, M. Lindeberg, R. W. Jackson, J. Selengut, R. Dodson et al., Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition, & other authors, vol.187, pp.6488-6498, 2005.

P. T. Johnson, J. C. De-roode, and A. Fenton, Why infectious disease research needs community ecology, Science, vol.349, 2015.

K. A. Jolley and M. C. Maiden, BIGSdb: Scalable analysis of bacterial genome variation at the population level, BMC Bioinformatics, vol.11, 2010.

K. Katoh and H. Toh, Recent developments in the MAFFT multiple sequence alignment program, Brief Bioinform, vol.9, pp.286-298, 2008.

, On: Mon, vol.55, p.21, 201706-01-30.

F. Krueger, Trim Galore!: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, 2015.

D. J. Lawson, G. Hellenthal, S. Myers, and D. Falush, Inference of population structure using dense haplotype data, PLoS Genet, vol.8, 2012.

W. Li, Y. Chiang, and G. Coaker, The HopQ1 effector's nucleoside hydrolase-like domain is required for bacterial virulence in arabidopsis and tomato, but not host recognition in Tobacco, PLoS ONE, vol.8, p.59684, 2013.

W. Li, K. A. Yadeta, J. M. Elmore, and G. Coaker, The Pseudomonas syringae Effector HopQ1 Promotes Bacterial Virulence and Interacts with Tomato 14-3-3 Proteins in a Phosphorylation-Dependent Manner, PLANT PHYSIOLOGY, vol.161, pp.2062-2074, 2013.

M. Lindeberg, C. R. Myers, A. Collmer, and D. J. Schneider, , 2008.

, Roadmap to new virulence determinants in Pseudomonas syringae: Insights from comparative genomics and genome organization, vol.21, pp.685-700

M. C. Maiden, M. J. Jansen-van-rensburg, J. E. Bray, S. G. Earle, S. A. Ford et al., MLST revisited: the gene-by-gene approach to bacterial genomics, Nat Rev Microbiol, vol.11, pp.728-736, 2013.

M. Martin, Cutadapt removes adapter sequences from highthroughput sequencing reads, EMBnet.journal, vol.17, p.10, 2011.

E. P. Martins and T. Garland, Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study, Evolution, vol.45, pp.534-557, 1991.

H. C. Mccann, E. H. Rikkerink, F. Bertels, M. Fiers, A. Lu et al., Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease, & other authors, vol.9, 2013.

S. M. Mccarter, J. B. Jones, R. D. Gitaitis, and D. R. Smitley, Survival of Pseudomonas syringae pv. tomato in association with tomato seed, soil, host tissue, and epiphytic weed hosts in Georgia, Phytopathology, vol.73, pp.1393-1398, 1983.

G. Méric, K. Yahara, L. Mageiros, B. Pascoe, M. C. Maiden et al., A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter, PLoS One, vol.9, 2014.

T. J. Mohr, H. Liu, S. Yan, C. E. Morris, J. A. Castillo et al.,

B. A. Vinatzer, Naturally occurring nonpathogenic isolates of the plant pathogen Pseudomonas syringae lack a type III secretion system and effector gene orthologues, J Bacteriol, vol.190, pp.2858-2870, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02666849

C. L. Monteil, C. Guilbaud, C. Glaux, F. Lafolie, and S. Soubeyrand,

C. E. Morris, Emigration of the plant pathogen Pseudomonas syringae from leaf litter contributes to its population dynamics in alpine snowpack, Environ Microbiol, vol.14, pp.2099-2112, 2012.

C. L. Monteil, R. Cai, H. Liu, M. E. Llontop, and S. Leman,

D. J. Studholme, C. E. Morris, and B. A. Vinatzer, Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens, New Phytol, vol.199, pp.800-811, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02648548

C. L. Monteil, M. Bardin, and C. E. Morris, Features of air masses associated with the deposition of Pseudomonas syringae and Botrytis cinerea by rain and snowfall, ISME J, vol.8, pp.2290-2304, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02637810

C. L. Monteil, F. Lafolie, J. Laurent, J. C. Clement, R. Simler et al.,

C. E. Morris, Soil water flow is a source of the plant pathogen Pseudomonas syringae in subalpine headwaters, Environ Microbiol, vol.16, pp.2038-2052, 2014.

C. E. Morris, C. Glaux, X. Latour, L. Gardan, R. Samson et al., The Relationship of host range, physiology, and genotype to virulence on cantaloupe in pseudomonas syringae from cantaloupe blight epidemics in France, Phytopathology, vol.90, pp.636-646, 2000.

C. E. Morris, D. C. Sands, B. A. Vinatzer, C. Glaux, C. Guilbaud et al., The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle, ISME J, vol.2, pp.321-334, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02666544

C. E. Morris, D. C. Sands, J. L. Vanneste, J. Montarry, B. Oakley et al., Inferring the evolutionary history of the plant pathogen Pseudomonas syringae from its biogeography in headwaters of rivers in North America, Europe, and New Zealand. MBio, vol.1, pp.107-117, 2010.

C. E. Morris, C. L. Monteil, and O. Berge, The life history of Pseudomonas syringae: linking agriculture to earth system processes, Annu Rev Phytopathol, vol.51, pp.85-104, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02652198

H. E. O'brien, S. Thakur, and D. S. Guttman, Evolution of plant pathogenesis in Pseudomonas syringae: a genomics perspective, Annu Rev Phytopathol, vol.49, pp.269-289, 2011.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

B. Pascoe, G. Meric, S. Murray, L. Mageiros, K. Yahara et al., Enhanced biofilm formation evolves from divergent genetic backgrounds in host generalist Campylobacter jejuni, Environ Microbiol, vol.17, pp.4779-4789, 2015.

L. J. Piddock, Multidrug-resistance efflux pumps -not just for resistance, Nat Rev Microbiol, vol.4, pp.629-636, 2006.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS One, vol.5, p.9490, 2010.

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice et al., Artemis: sequence visualization and annotation, Bioinformatics, vol.16, pp.944-945, 2000.

S. K. Sheppard, K. A. Jolley, and M. C. Maiden, A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter, Genes, vol.3, pp.261-277, 2012.

S. K. Sheppard, X. Didelot, G. Meric, A. Torralbo, K. A. Jolley et al., Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter, Proc Natl Acad Sci U S A, vol.110, pp.11923-11927, 2013.

R. P. Singh, D. P. Hodson, J. Huerta-espino, Y. Jin, S. Bhavani et al., The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production, Annu Rev Phytopathol, vol.49, pp.465-481, 2011.

C. Struve and K. A. Krogfelt, Pathogenic potential of environmental Klebsiella pneumoniae isolates, Environ Microbiol, vol.6, pp.584-590, 2004.

E. H. Stukenbrock and B. A. Mcdonald, The origins of plant pathogens in agro-ecosystems, Annu Rev Phytopathol, vol.46, pp.75-100, 2008.

A. P. Tampakaki, N. Skandalis, A. D. Gazi, M. N. Bastaki, P. F. Sarris et al., , 2011.

, Harp": evolution of our understanding of hrp/hrc genes, Annu Rev Phytopathol, vol.48, pp.347-370

B. A. Vinatzer, C. L. Monteil, and C. R. Clarke, Harnessing population genomics to understand how bacterial pathogens emerge, adapt to crop hosts, and disseminate, Annu Rev Phytopathol, vol.52, pp.19-43, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02636703

C. F. Wei, B. H. Kvitko, R. Shimizu, E. Crabill, J. R. Alfano et al., A Pseudomonas syringae pv, 2007.

, Downloaded from www.microbiologyresearch

, 55:21 is able to cause disease in the model plant Nicotiana benthamiana, Plant J, vol.51, pp.32-46, 201706-01-30.

H. Whiley, B. Van-den-akker, S. Giglio, and R. Bentham, The role of environmental reservoirs in human campylobacteriosis, Int J Environ Res Public Health, vol.10, pp.5886-5907, 2013.

M. E. Woolhouse, L. H. Taylor, and D. T. Haydon, Population biology of multihost pathogens, Science, vol.292, pp.1109-1112, 2001.

X. F. Xin and S. Y. He, Pseudomonas syringae pv. tomato DC3000: a model pathogen for probing disease susceptibility and hormone signaling in plants, Annu Rev Phytopathol, vol.51, pp.473-498, 2013.

K. Yahara, Y. Furuta, K. Oshima, M. Yoshida, T. Azuma et al., Chromosome painting in silico in a bacterial species reveals fine population structure, Molecular Biology and. Evolution, vol.30, pp.1454-1464, 2013.

K. Yahara, X. Didelot, M. A. Ansari, S. K. Sheppard, and D. Falush, Efficient inference of recombination hot regions in bacterial genomes, Mol Biol Evol, vol.31, pp.1593-1605, 2014.

K. Yahara, X. Didelot, K. A. Jolley, I. Kobayashi, and M. C. Maiden,

S. K. Sheppard and D. Falush, The landscape of realized homologous recombination in pathogenic bacteria, Mol Biol Evol, vol.33, pp.456-471, 2016.

K. Yahara, A. Taylor, S. De-vries, S. Murray, B. Pascoe et al., Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork, & other authors, vol.4, 2016.

S. Yan, H. Liu, T. J. Mohr, J. Jenrette, R. Chiodini et al., Role of recombination in the evolution of the model plant pathogen Pseudomonas syringae pv. tomato DC3000, a very atypical tomato strain, Applied and Environmental. Microbiology, vol.74, pp.3171-3181, 2008.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-829, 2008.