Pangenome Analysis Uncovers Two Pathotypes of Dickeya dadantii, the Causal Agent of Sweetpotato Stem Rot, and Identifies Virulence-Associated Genes.
TL;DR
The first comprehensive pangenome of D. dadantii is constructed by integrating complete PacBio HiFi sequencing of a representative strain with resequencing of 32 Chinese isolates and 23 global strains, revealing that geographic isolation and host adaptation drive genetic differentiation.
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.