Comparative Genomic Analysis of the Lettuce Bacterial Leaf Spot Pathogen, pv. , to Investigate Race Specificity.

Bacterial leaf spot (BLS) of lettuce caused by pv. () was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen strains representing the three races, along with eight related strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the races. Genome sequences were mined for effector genes, which have been shown to be involved in race specificity in other systems. Two effectors identified in this study, and the novel variant , were revealed as possible mediators of a gene-for-gene interaction between race 1 and 3 strains and wild lettuce ARM-09-161-10-1. Transposase sequence identified downstream of and prophage sequence found nearby within race 1 and 3 insertion sequences suggest that this gene may have been acquired through phage-mediated gene transfer. No other factors were identified from these analyses that distinguish the races.