Comparative genomic analysis of Herbaspirillum strains associated with banana sheath rot reveals potential virulence...

Banana (Musa spp.) is a critical global fruit crop whose production is severely threatened by sheath rot disease. Klebsiella variicola has been identified as one of the main causative agents of this disease, while the pathogenicity of Herbaspirillum spp. strains isolated from sheath rot-infected banana tissues remains to be clearly defined.

We isolated five Herbaspirillum strains from infected banana sheaths, namely Herbaspirillum huttiense Musa1 (hereafter abbreviated as Her1), Herbaspirillum huttiense Musa2 (hereafter Her2), Herbaspirillum sp. Musa3 (hereafter Her3), Herbaspirillum huttiense Musa4 (hereafter Her4), and Herbaspirillum huttiense Musa5 (hereafter Her5), and performed whole-genome sequencing on each isolate. Comparative genomics revealed genomes of similar size and stable GC content across strains. Functional annotation uncovered a core set of carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs), indicating conserved metabolic capabilities. Notably, two pectate lyase genes, potentially involved in plant cell wall degradation, were uniquely identified in strain Her3. We observed marked variation in the repertoire of putative virulence determinants across the isolates: strains Her1 and Her4 each encoded 17 predicted type III secretion system (T3SS) effector proteins, a notably higher number than that of the other strains. All strains also harbored a substantial number of predicted type VI secretion system (T6SS) effectors.

This study provides the first genomic resource for Herbaspirillum species associated with banana sheath rot. Our comparative analysis highlights key genomic differences, particularly in secreted effector profiles, that likely underlie strain-specific pathogenic mechanisms. These results enhance our fundamental understanding of the phytopathogenicity of Herbaspirillum in plants.