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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2310-x) contains supplementary material, which is available to authorized users.

Xanthomonas citri pv. citri Pathotypes: LPS Structure and Function as Microbe‐Associated Molecular Patterns

“…Pathotype A is the most widespread and has the broadest host range: it infects almost all Citrus species as well as some other plants of the Rutaceae family . Based on single nucleotide polymorphism data from short‐read genomic data, pathotype A strains are classified into several clusters; one, DAPC1, is predominantly associated with the major geographical expansion of the pathogen from its origin during the twentieth century . Pathotypes A* and A W show a narrow host range, restricted mostly to Mexican lime ( Citrus aurantifolia ) and its close relative Citrus macrophylla , although some strains were found mildly pathogenic to a few additional citrus species .…”

“…Based on single nucleotide polymorphism data from short‐read genomic data, pathotype A strains are classified into several clusters; one, DAPC1, is predominantly associated with the major geographical expansion of the pathogen from its origin during the twentieth century . Pathotypes A* and A W show a narrow host range, restricted mostly to Mexican lime ( Citrus aurantifolia ) and its close relative Citrus macrophylla , although some strains were found mildly pathogenic to a few additional citrus species . The reasons for the differences in host range between the pathotypes are not fully defined.…”

“…The reasons for the differences in host range between the pathotypes are not fully defined. Gordon et al . identified genomic differences between these pathotypes, and they suggested several candidate genes associated with host range and various aspects of virulence.…”

Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas

“…A role of two T3Es (AvrBsT and XopQ) in shaping the host range of Xanthomonas perforans among solanaceous species has recently been revealed (117). However, within pathovars, the picture is much more complicated: Whereas in some cases T3E variations observed within a pathovar were linked to the host of isolation of the strains (57,58), in other cases no correlation could be observed between T3E variations and pathotypes or races (12,51,55,112). These results highlight the complexity of the genetic basis of host specificity in plant-pathogenic bacteria.…”

Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity

“…From the present study, we report the genomes of 18 reference pathovar strains of XCPs and compare them with those of 4 publicly available XCPs (46)(47)(48)(49). However, these XCPs have historically been classified into three different species of Xanthomonas and one of these strains has been assigned to another genus, Pseudomonas ( Table 1).…”