Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida

Abstract

Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be “core” genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida.

Recently emerged and diverse lineages of Xanthomonas perforans have independently evolved through plasmid acquisition and homologous recombination originating from multiple Xanthomonas species

“…1). Sequence clusters (SCs) 1 through 4 corresponded to the previously described population structure of X. perforans strains collected in Florida (19, 20), while SCs 5 and 6 were composed exclusively of Alabama strains sequenced in this study. Each of the genetic clusters inferred in this analysis were primarily clonal within the lineage, except for SC2 (referred to as Group 1b by Schwartz et al (20), which exhibited diversity.…”

“…Likewise, temporal shifts in the species and pathogen races (as determined by gene for gene interactions) responsible for the disease in specific tomato and pepper production regions have been documented over the years (12, 14). Although these fluxes in the pathogen population are subject to random genetic drift associated with patterns of international trade, evolutionary and ecological factors such as horizontal gene transfer, homologous recombination, and interspecific competition via the production of antagonistic bacteriocins are also significant factors contributing to these population dynamics (15–19). Therefore, bacterial leaf spot presents an attractive model system enabling the investigation of adaptive evolution in a bacterial population mediated by recombination, host selection pressure, and interspecific competition.…”

“…Currently, X. perforans can be divided into three different phylogenetic groups (19). Until the isolation of a single X. perforans strain from an infected pepper sample during the 2010 season in Florida (20), the host-range of this bacterial pathogen was thought to be restricted to tomato.…”

“…This observation led to subsequent investigations which revealed that in the absence of effector triggered immunity induced by a single avirulence gene (either avrBsT or avrXv3 ), X. perforans strains representative of the three phylogenetic groups differed in their ability to multiply and cause disease when infiltrated into pepper leaves (20). Intriguingly, genomes of the pepper-pathogenic, group 2 X. perforans strains displayed evidence of extensive recent recombination originating from X. euvesicatoria (which is the predominant pathogen of pepper), whereas similar signatures were reported to be minimal among the group 1, tomato-limited strains (13, 19).…”

“…The strains that belong to this larger phylogenetic group were classified into several species including X. alfalfae , X. axonopodis , X. perforans and X. euvesicatoria and are associated with diseases of diverse monocot and dicotyledonous plant families (23). While the importance of homologous recombination in facilitating the emergence of novel X. perforans lineages has been established (18, 19), the extent of genetic exchange across the larger X. euvesicatoria species complex and specific functional pathways affected by homologous recombination remains to be explored.…”