Population Structure of <i>Xanthomonas citri</i> pv. <i>citri</i> in Iran: 1991 - 2022

Citrus canker, caused by <i>Xanthomonas citri</i> pv. <i>citri</i>, is one of the most devastating bacterial diseases of citrus species. The global population of <i>Xanthomonas citri</i> pv. <i>citri</i> includes three lineages designated as pathotypes A, A* and A^w. While pathotype A is the most prevalent lineage around the world, the citrus canker pathogen in Iran includes only pathotype A* strains. Previous work on the <i>Xanthomonas citri</i> pv. <i>citri</i> strains collected before 2013 showed that two lineages of the pathogen presented in Iran, i.e., 4.1 and 4.4, with 4.4 not present anywhere else at that time. In this study, using a new set of strains collected in 2021-2022, we re-assessed the population structure of the pathogen in Iran using a phylogeographic approach. All strains isolated in Iran still belonged to pathotype A*. Multilocus variable number tandem repeat analysis (MLVA) revealed that 62 Iranian strains collected between 1991-2022 were distributed among 22 haplotypes. Four new haplotypes were identified within the strains isolated in this study which have not previously been reported elsewhere in the world. Although all pre-2013 strains isolated in Sistan-Baluchestan Province of Iran were grouped in subcluster 4.4, all post-2020 strains isolated in the same area were identified as members of subcluster 4.1. None of the post-2020 strains isolated in Iran belonged to subcluster 4.4, which suggests a shift in population structure of the pathogen over the past two decades. Our data would pave the way of research on the population structure of citrus canker pathogen in the area.