An Environmental Strain of <i>Pantoea ananatis</i> (SK-1) Is Capable of Onion Necrosis but Is Sensitive to Thiosulfinates

Pantoea ananatis is a widely distributed bacterium and is one of the causal agents of onion center rot, a disease responsible for significant global yield losses. While the environmental isolate P. ananatis SK-1, recovered from the Shirakawa River, Japan, is known to induce tissue necrosis in onion, the genetic basis of its pathogenicity remained uncharacterized. In this study, we generated a high-quality hybrid genome assembly of SK-1 using Oxford Nanopore and Illumina sequencing, yielding a 5.0 Mb genome across three contigs with 100% completeness as determined by CheckM. Genomic analysis identified a highly conserved HiVir (high virulence) cluster, a known pathogenicity gene cluster in onion-pathogenic Pantoea spp. However, the alt (allicin tolerance) cluster, which is responsible for imparting tolerance to thiosulfinates in onion tissue, was absent. Functional assays demonstrated that deletion of pepM, a key gene in the HiVir cluster, abolished necrosis in onion tissues, while complementation restored pathogenesis. In contrast, SK-1 exhibited reduced growth in onion juice, consistent with increased sensitivity to thiosulfinates that supports the lack of alt cluster in the bacterium. These findings indicate that although SK-1 possesses onion-pathogenic potential, it lacked the ability to proliferate in onion tissue, suggesting a limited capacity to rot onion.