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

BMC Genomics

Research Article

Stéphane Cruveiller¹  Valérie Barbe¹  Aline Escalon²  Pierre Lefeuvre²  Olivier Pruvost²  Lionel Gagnevin³  Jonathan L. Gordon⁴ 

[1] CEA/DSV/IG/Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France;CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France;CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France;Current Address: UMR IPME, IRD-CIRAD-Université Montpellier, 34394, Montpellier, France;Université de la Réunion, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France;Current Address: CIRAD, UMR CMAEE, F-97170, Petit-Bourg, Guadeloupe, France;

关键词: Xanthomonas citri;    Plant pathogen;    Genome evolution;    Pathotype evolution;    Host range determination;    Recombination;    Gene islands;    Ancestral character estimation;    Pathogenicity;    Gene presence/absence;   

DOI  :  10.1186/s12864-015-2310-x

 received in 2015-08-21, accepted in 2015-12-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Gordon et al. 2015