New Genomes of Xanthomonas citri pv. bilvae from Modern and Historical Material Reveal the History and Genomics of a Neglected Crop Pathogen.

In this study, we present novel genomic data for Xanthomonas citri pv. bilvae (Xcb), the causal agent of bacterial shot-hole disease in bael trees. Using a hybrid sequencing approach that combines short- and long-read technologies, we assembled high-quality genomes of the only two available contemporary Xcb strains. Furthermore, we reconstructed the first historical genome of Xcb from a herbarium specimen collected in 1848, thereby extending the documented presence of this overlooked disease in India by nearly 100 years. We then characterized the genomic features of these strains, with a particular emphasis on virulence factors and plasmid content, using a suite of specialized bioinformatics tools. The contemporary Xcb strains were found to carry between one and four plasmids, which varied in their mobility potential (conjugative, mobilizable, or non-mobile). A total of 30 to 32 type III effector (T3E) genes were identified across chromosomes and plasmids. Notably, one of the contemporary strains harbored four plasmid-borne transcription activator-like effectors (TALEs), which showed only distant similarity to TALEs found in X. citri pv. citri, a globally major pathogen with a partially overlapping host range. Comparative genomic analysis between the contemporary and historical strains revealed a remarkable conservation of effector gene content, indicating that key pathogenic traits may have been acquired early in Xcb’s evolutionary history. Collectively, these new genomic resources provide valuable insights into the biology and evolution of this underexplored bacterial pathogen.