Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Gordon Jonathan, Lefeuvre Pierre, Escalon Aline, Barbe Valérie, Cruveiller Stéphane, Gagnevin Lionel, Pruvost Olivier. 2015. Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. BMC Genomics, 16 (1098), 20 p.

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Abstract : Background The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. Results The strains from each pathotype form monophyletic clades, with a short branch shared by the Aw and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, Aw and A/Aw clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and Aw are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences. Conclusions The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them.

Mots-clés Agrovoc : Xanthomonas campestris citri, Pathotype, Plante hôte, Génie génétique, Gène, Génome, Évolution, Phylogénie, Carte génétique, Recombinaison, Pouvoir pathogène, Adaptation

Mots-clés géographiques Agrovoc : Monde, France, Réunion

Mots-clés complémentaires : Xanthomonas citri pv citri

Classification Agris : H20 - Plant diseases

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Agence(s) de financement européenne(s) : European Commission

Programme de financement européen : FP7

Projet(s) de financement européen(s) : Supporting the research potential on emerging infectious diseases in La Réunion Island, an EU outermost region in the South-Western Indian Ocean

Auteurs et affiliations

  • Gordon Jonathan, CIRAD-BIOS-UMR CMAEE (GLP)
  • Lefeuvre Pierre, CIRAD-BIOS-UMR PVBMT (REU)
  • Escalon Aline
  • Barbe Valérie, Centre national de séquençage (FRA)
  • Cruveiller Stéphane, Centre national de séquençage (FRA)
  • Gagnevin Lionel, CIRAD-BIOS-UMR IPME (FRA)
  • Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)

Source : Cirad-Agritrop (

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