Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen

Abstract

Pseudomonas syringae is a common foliar bacterium responsible for many important plant diseases. We studied the population structure and dynamics of the core genome of P. syringae via multilocus sequencing typing (MLST) of 60 strains, representing 21 pathovars and 2 nonpathogens, isolated from a variety of plant hosts. Seven housekeeping genes, dispersed around the P. syringae genome, were sequenced to obtain 400 to 500 nucleotides per gene. Forty unique sequence types were identified, with most strains falling into one of four major clades. Phylogenetic and maximum-likelihood analyses revealed a remarkable degree of congruence among the seven genes, indicating a common evolutionary history for the seven loci. MLST and population genetic analyses also found a very low level of recombination. Overall, mutation was found to be approximately four times more likely than recombination to change any single nucleotide. A skyline plot was used to study the demographic history of P. syringae. The species was found to have maintained a constant population size over time. Strains were also found to remain genetically homogeneous over many years, and when isolated from sites as widespread as the United States and Japan. An analysis of molecular variance found that host association explains only a small proportion of the total genetic variation in the sample. These analyses reveal that with respect to the core genome, P. syringae is a highly clonal and stable species that is endemic within plant populations, yet the genetic variation seen in these genes only weakly predicts host association.

FIG. 1.

Schematic representation of the positions of the seven housekeeping genes used in this study, based on the sequenced P. syringae pv. tomato DC3000 genome (NCBI accession no. NC_004578). The position of each locus (in base pairs) is given below the gene name.

FIG. 2.

NJ tree of the concatenated data set. The four major groups discussed in the text are labeled. The host of isolation is given next to each strain designation. Bootstrap scores greater than 60 are given at each node. PfK756 is a P. fluorescens strain used as an outgroup.

FIG. 3.

Split decomposition analysis of each housekeeping gene. Bootstrap scores greater than 60 are given at each node. Significant reticulations are those in which there is a roughly equal high level of support for alternative paths in the graph.

FIG. 4.

Split decomposition analysis of the concatenated data set. The four major groups discussed in the text are indicated. Bootstrap scores greater than 60 are given at each node.

FIG. 5.

Sliding-window analysis of polymorphism (thin lines) and divergence from P. fluorescens (heavy lines) for each of the seven housekeeping genes.

FIG. 6.

Skyline plot of the concatenated data set.