Evolutionary genomics of host specificity in the plant pathogen Pseudomonas syringae

Changes in host specificity are responsible for emerging diseases, yet the biology of bacterial host specificity is poorly understood. The goal of studies initiated in this thesis is to understand the genomic and evolutionary bases of host specific virulence in the model plant pathogen Pseudomonas syringae. P. syringae is ideal for host specificity studies because as a species it causes disease on a wide diversity of crops, but individual isolates typically have a very limited disease host range.; I have used a functional evolutionary genomics approach to identify host specific virulence genes and address their evolution. First, I genotyped natural isolates of P. syringae isolates from different plant hosts by multilocus sequence typing (MLST) of 7 housekeeping genes that represent the core genome. This provided a robust species phylogeny and demonstrated that P. syringae is clonal and endemic. The vertically transferred core genome was only weakly associated with pathogen host specificity, supporting the alternative explanation that horizontally transferred flexible genes determine host specificity.; Second, using a functional genetic screen, I contributed to the identification of the largest known arsenal of virulence genes directly injected by pathogens into their hosts by the type III secretion system. These type III secreted effectors (T3SEs) were variably distributed among strains in a pattern inconsistent with the core phylogeny, suggesting their horizontal transfer.; Third, I hypothesized that horizontal transfer of T3SE genes results in gene constellations that determine a strain's host specificity. I determined the distribution of T3SEs and other virulence genes in natural isolates of P. syringae by comparative genomic hybridization. Over 22 T3SEs have been identified as putative host specificity genes. Mapping of this data onto the core phylogeny showed that acquisition by horizontal gene transfer of several T3SE genes is associated with a host shift to tomato and Brassica crops.; These studies identify putative host specificity genes and demonstrate that P. syringae may use multiple strategies for infecting the same host. This novel approach can be used in other pathogens, provides targets for antimicrobial development, and contributes important information for predictive management of emerging diseases.