AUTHOR=Timilsina Sujan , Pereira-Martin Juliana A. , Minsavage Gerald V. , Iruegas-Bocardo Fernanda , Abrahamian Peter , Potnis Neha , Kolaczkowski Bryan , Vallad Gary E. , Goss Erica M. , Jones Jeffrey B. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00448

DOI=10.3389/fmicb.2019.00448

ISSN=1664-302X

ABSTRACT=<p>Prior to the identification of <italic>Xanthomonas perforans</italic> associated with bacterial spot of tomato in 1991, <italic>X. euvesicatoria</italic> was the only known species in Florida. Currently, <italic>X. perforans</italic> is the <italic>Xanthomonas</italic> sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant <italic>X. perforans</italic> genotype in Florida. We previously reported recombination of <italic>X. perforans</italic> strains with closely related <italic>Xanthomonas</italic> species as a potential driving factor for <italic>X. perforans</italic> evolution. However, the extent of recombination across the <italic>X. perforans</italic> 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 <italic>X. perforans</italic>. A total of 1,356 genes were determined to be “core” genes conserved among the 58 <italic>X. perforans</italic> genomes used in the study. Our approach identified three genetic groups of <italic>X. perforans</italic> 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 <italic>X. euvesicatoria</italic>, 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 <italic>X. perforans</italic> in Florida.</p>