Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex

Abstract

Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from the P. syringae species complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in the P. syringae pan-genome, reconstruct the phylogeny of P. syringae using a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that \"ecologically significant\" virulence-associated loci and \"evolutionary significant\" loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.