The Distinct Genomic Architecture of Pectobacterium brasiliense Strain BS1113, a Soft Rot Pathogen of Cigar Tobacco Lacking a Type III Secretion System

Background The bacterium Pectobacterium brasiliense causes severe soft rot disease across a wide variety of plant hosts. Although the genome of the reference strain SX309 has been characterized, the molecular basis of pathogenicity in isolates adapted to cigar tobacco has not yet been investigated.This study presents a comparative genomic and pathogenicity analysis of P. brasiliense strain BS1113, isolated from cigar tobacco, to elucidate its unique adaptive features. Results Here we report the complete genome sequence of strain BS1113, which comprises 4.92 Mb with a G + C content of 51.96%. Comparative analysis against the closely related strain SX309 revealed the absence of an intact type III secretion system (T3SS) gene cluster in BS1113, despite T3SS being a canonical virulence determinant in numerous Gram-negative pathogens, Despite this absence, BS1113 retains a highly conserved arsenal of virulence factors, including plant cell wall-degrading enzymes (PCWDEs) and their dedicated type II secretion system (T2SS), along with quorum-sensing systems. Furthermore, the genome harbors variable regions encoding a type VI secretion system (T6SS) and a subtype I-F CRISPR-Cas system, implying roles in for host interaction and adaptive immunity. Conclusions The lack of T3SS in BS1113 points to a distinct evolutionary trajectory towards niche specialization. Its pathogenic strategy may depend on opportunistic invasion through wounds and rapid tissue degradation mediated by T2SS‑delivered PCWDEs, diverging from the effector‑dependent immunosuppression employed by T3SS‑containing relatives such as SX309. Our findings highlight significant intra-species genomic diversity within P. brasiliense and uncover a distinct pathogenic architecture in strain BS1113, offering fresh insights on the adaptive evolution of soft rot pathogens.