Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology

Abstract

A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.

Keywords: Pseudomonas syringae; evolution; mutation; natural selection; population structure; recombination; species definition.

Figure 1

Phylogenetic tree and type III secretion system distribution of Pseudomonas syringae type and pathotype strains. Maximum likelihood phylogenetic analysis of the P. syringae species complex including 62 type (T) and pathotype (PT) strains, as well as the three strains with finished (FG) genomes. Type strains are isolates to which the scientific name of that organism is formally attached under the rules of prokaryote nomenclature. Pathotype strains are similar to type strains, with the additional requirement that a pathotype strain has the pathogenic characteristics of its pathovar (for details, see Thakur et al., 2016). Phylogroup (PG) designations are indicated on the appropriate branches. The distribution of the four type III secretion systems is shown to the right: canonical (tripartite pathogenicity island, T‐PAI), rhizobial (R‐PAI), single (S‐PAI) and atypical‐A (A‐PAI).

Figure 2

Type III secretion systems (TTSSs) across Pseudomonas syringae. At the top of the figure, one representative drawing is displayed for each known type III secretion class found within P. syringae sensu lato strains. Representations were adapted from the genomic annotations of the following strains: canonical (T‐PAI), P. syringae pv. tomato DC3000 (GenBank AE016853.1); rhizobial (R‐PAI), P. syringae pv. phaseolicola 1448a (GenBank CP000058.1); S‐PAI, P. viridiflava LMCA8 (GenBank JXQO00000000.1); atypical‐A, P. syringae Psy508 (GenBank ADGB00000000.1); atypical‐B, P. syringae UB246 (GenBank AVEQ00000000.1). The positions of select genes in the TTSS and border regions, as well as tRNA loci in proximity, are annotated within each drawing. The bottom of the figure displays the genomic context for each TTSS, using P. syringae pv. tomato DC3000 as a reference. Anchor points for genomic context were identified by manual inspection of genes outside of the TTSS of interest in its native genome (see above) as regions in which multiple open reading frames (ORFs) are conserved between the native genome and P. syringae pv. tomato DC3000. The ‘Atypical‐B’ TTSS is split across multiple contigs in the genome assembly of UB246, and anchor points were identified through inspection of identical contigs from genome sequences for closely related strains (D. A. Baltrus, unpublished data).