Phylogenetic Diversity and Clonal Expansion in the <i>Ralstonia solanacearum</i> Species Complex: A Case Study With Bacterial Wilt Outbreak in Eggplant

ABSTRACT The Ralstonia solanacearum species complex (RSSC) is a major plant pathogen causing bacterial wilt in solanaceous vegetables and many economically important crop plants. In this study, nine bacterial isolates from wilt‐affected eggplant and tomato plants in Tamil Nadu were characterised by a polyphasic approach. All isolates induced complete wilting of test eggplant and tomato plants within 3–4 days post‐inoculation, indicating high virulence. Molecular identification via 16S rRNA sequencing and species‐specific primers confirmed them as R . pseudosolanacearum ; multiplex PCR assigned them to Phylotype I. Multilocus sequence typing (MLST) of five housekeeping ( adk , gapA , gyrB , ppsA , gdhA ) and two virulence genes ( egl , fliC ) revealed a high degree of genetic conservation, with most alleles identical across strains. Minor variations in ppsA and egl suggested novel alleles in three isolates. MLST analysis grouped the isolates into six clusters; Cluster I showed high similarity, Clusters III and IV exhibited allelic variation. Sequence polymorphism analysis across four phylotypes showed moderate genetic diversity within Phylotype I, indicating a genetically stable but clonally diverse population. Phylotype II exhibited slightly higher nucleotide diversity but reduced haplotype diversity, suggesting population contraction or selective constraints. Phylotype III, despite being represented by only five isolates, showed the highest nucleotide diversity and frequent recombination, reflecting a dynamic and evolving lineage. Phylotype IV displayed intermediate levels of diversity with fewer recombination events, indicating a more stable population structure. These findings emphasise the clonal structure, regional adaptation and evolutionary patterns of RSSC strains, highlighting the need for continued genomic surveillance to inform disease management strategies.