Phylogenomic sequence analysis of Xanthomonas citri pathovars anacardii and mangiferaeindicae reveals a diversity of pathogenicity factors.

Xanthomonas citri comprises of phytopathogenic pathovars that can cause disease in mangoes and cashews. Xanthomonas citri pv. mangiferaeindicae (Xcm) causes mango bacterial black spot and X. citri pv. anacardii (Xca) causes cashew bacterial black spot. Currently, there are a limited number of complete genomes available for these pathovars, which hinders pathogenicity studies. In this study, we collected 53 isolates of Xcm and Xca from mango hosts and generated 50 Xcm (18 complete and 32 scaffold level) and 3 complete non-pigmented Xca genome assemblies using Illumina and Nanopore sequencing. We used comparative genomics to identify virulence-associated genes of both pathovars, and found transcription activator-like effectors (TALEs), which aid in host-plant infection, were present in complete and circularized assemblies of Xcm. One to three plasmids were identified amongst the complete Xcm assemblies, while no plasmids were observed in Xca. Analysis of complete and circularized genomes revealed the presence of 14 TAL classes either in chromosome or plasmid positions. Amongst them only the TalKC class was shared across all strains. Although, no plasmid was found in Xca, the TalKS class genes were found in the bacterial chromosome. Virulence associated genes varied at the interspecies level, with Xca and Xcm shown to have distinct sets of type III effectors. We observed that xopB, xopAG2 and xopAM were present in all Xca strains but absent in Xcm. In contrast, xopAW were present in all Xcm but absent in Xca. Further functional investigation of these genes could reveal those that play a critical role in pathogenicity and/or host specificity.