Pangenome Analysis Uncovers Two Pathotypes of Dickeya dadantii , the Causal Agent of Sweetpotato Stem Rot, and Identifies Virulence-Associated Genes

Abstract

Bacterial stem and root rot (BSRR), caused by Dickeya dadantii, is a devastating disease affecting sweetpotato [Ipomoea batatas (L.) Lam.] worldwide, yet the pathogen’s population structure and core virulence determinants remain poorly understood. Here, we constructed the first comprehensive pangenome of D. dadantii by integrating complete PacBio HiFi sequencing of a representative strain (E36) with resequencing of 32 Chinese isolates and 23 global strains. Population genomic analysis revealed that geographic isolation and host adaptation drive genetic differentiation, with sweetpotato-associated Chinese strains clustering into two major lineages (Groups I and II). Mining the core genome identified 36 conserved candidate effectors, of which CpxP and Spy were experimentally validated as virulence factors: both triggered a hypersensitive response in Nicotiana benthamiana, and their deletion mutants exhibited attenuated virulence on sweetpotato. This study delineates the population architecture of the BSRR pathogen and uncovers key virulence determinants.