Distinct Lineages of <i>Pantoea ananatis</i> Associated with Rice Differ in Toxin Biosynthesis Gene Content and Host Specialization

Pantoea ananatis has recently emerged as a causal agent of Pantoea leaf blight (PLB) and Pantoea panicle blight (PPB) of rice in the United States, raising concerns about its potential impact on rice production. Despite increasing reports of the disease, mechanisms underlying host specialization and virulence within this pathosystem remain poorly understood. Here, we combined comparative genomics and in-planta assays to investigate population structure and virulence determinants among rice-associated P. ananatis strains. Average nucleotide identity analysis of P. ananatis genomes resolved two lineages with contrasting host associations. One lineage, composed of strains recovered almost exclusively from rice, lacked the HiVir operon responsible for synthesis of the phosphonate toxin pantaphos. A second, broadly distributed lineage included P. ananatis isolated from diverse hosts, including rice, and many contained the HiVir operon. HiVir-mediated pantaphos production induced necrotic symptom development, but was not required for bacterial replication within rice tissue. Accordingly, strains lacking HiVir, including those from the rice-associated lineage and targeted mutants, exhibited reduced necrosis while achieving bacterial population sizes comparable to wild-type generalist strains during infection of rice. Conversely, host-range experiments showed that rice-associated strains colonized onion tissue less than generalist strains, consistent with evolutionary specialization for rice. Comparative pangenome analysis supported the separation of lineages and identified hundreds of lineage-specific genes that may underpin host associations. These findings demonstrate that P. ananatis populations associated with rice comprise distinct evolutionary lineages with differing genomic features and virulence strategies and reveal a decoupling between symptom development and bacterial proliferation during infection of rice.