Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana

Abstract

Species-level genetic diversity and recombination in bacterial pathogens of wild plant populations have been nearly unexplored. Pseudomonas viridiflava is a common natural bacterial pathogen of Arabidopsis thaliana, for which pathogen defense genes and mechanisms are becoming increasing well known. The genetic variation contained within a worldwide sample of P. viridiflava collected from wild populations of A. thaliana was investigated using five genomic sequence fragments totaling 2.3 kb. Two distinct and deeply diverged clades were found within the P. viridiflava sample and in close proximity in multiple populations, each genetically diverse with synonymous variation as high as 9.3% in one of these clades. Within clades, there is evidence of frequent recombination within and between each sequenced locus and little geographic differentiation. Isolates from both clades were also found in a small sample of other herbaceous species in Midwest populations, indicating a possibly broad host range for P. viridiflava. The high levels of genetic variation and recombination together with a lack of geographic differentiation in this pathogen distinguish it from other bacterial plant pathogens for which intraspecific variation has been examined.

Figure 1.—

Consensus of 14,000 trees generated by Bayesian inference for the concatenated data set. Branch length values represent only trees on which those branches were present. Posterior probabilities (×100) of clades are given. The tree was rooted with three P. syringae sequences (Pph 1448a, Psy B728a, and Pto DC3000). Isolates collected from other host species in A. thaliana populations are shown in italics.

Figure 2.—

Consensus of 2000 trees generated by Bayesian inference for gyrB. Branch length values represent only trees on which those branches were present. Posterior probabilities (×100) of clades are given. The tree was rooted with P. syringae sequences as in Figure 1. Arrows indicate the P. viridiflava isolates sequenced by Yamamoto et al. (2000).

Figure 3.—

Split decomposition networks for the five sequence fragments. Solid circles are clade A haplotypes, and open circles are clade B haplotypes. Bootstrap scores >80% are shown.