Molecular epidemiology of the citrus bacterial pathogen Xanthomonas citri pv. citri from the Arabian Peninsula reveals a complex structure of specialist and generalist strains

Abstract

Molecular epidemiology studies are essential to refine our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence, and to understand the factors that shape their population structure. Microsatellite and minisatellite typing are useful techniques for deciphering the population structure of Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. This paper presents a molecular epidemiology study, which has improved our understanding of the history of the pathogen's introductions into the Arabian Peninsula, since it was first reported in the 1980s. An unexpectedly high genetic diversity of the pathogen was revealed. The four distinct genetic lineages within X. citri pv. citri, which have been reported throughout the world, were identified in the Arabian Peninsula, most likely as the result of multiple introductions. No copper-resistant X. citri pv. citri strains were identified. The pathogen's population structure on Mexican lime (their shared host species) was closely examined in two countries, Saudi Arabia and Yemen. We highlighted the marked prevalence of specialist pathotype A* strains in both countries, which suggests that specialist strains of X. citri pv. citri may perform better than generalist strains when they occur concomitantly in this environment. Subclade 4.2 was the prevailing lineage identified. Several analyses (genetic structure deciphered by discriminant analysis of principal components, R_ST-based genetic differentiation, geographic structure) congruently suggested the role of human activities in the pathogen's spread. We discuss the implications of these results on the management of Asiatic citrus canker in the region.

Keywords: bacterial disease; citrus; host specialization; microsatellites; minisatellites; molecular epidemiology.

FIGURE 1

(a) Map of the Arabian Peninsula showing the three regions from Saudi Arabia and the three governorates from Yemen where citrus canker samples were collected (including the number of authenticated Xanthomonas citri pv. citri strains and their genetic assignation). Note that the exact isolation place is unknown for Omanese strains from a previous study (Vernière et al., 1998). (b) Close‐up map. Blue solid lines link pairs of subclade 4.2 local populations (blue dots) for which no significant genetic differentiation (p > 0.05 based on R_ST) was found.

FIGURE 2

Minimum spanning tree from MLVA‐14 data showing the genetic diversity of Xanthomonas citri pv. citri in the Arabian Peninsula. All strains from distinct networks or singletons differed at ≥6 microsatellite loci. Dots represent haplotypes. Dot diameter and color are representative of the number of strains per haplotype, country, and host of isolation, respectively (light green: Saudi Arabia from Mexican lime; dark green: Saudi Arabia from other citrus; light blue: Yemen from Mexican lime; dark blue: Yemen from other citrus). Oman strains from a previous study (Vernière et al., 1998) are shown as red dots.

FIGURE 3

Genetic structure of Xanthomonas citri pv. citri subclade 4.2 originating from Saudi Arabia and Yemen based on the discriminant analysis of principal components (DAPC) of microsatellite data. Numbers and colors represent the seven genetic clusters retained from Bayesian information criterion (BIC) values. Clockwise: (a) scatterplot representing axes 1 and 2 of the DAPC; (b) scatterplot representing axes 1 and 3 of the DAPC; (c) scatterplot representing axes 1 and 4 of the DAPC; (d) scatterplot representing axes 1 and 5 of the DAPC.