Genomic characteristics and virulence genes of Pseudomonas glycinae, the causal agent of bacterial soft rot in ginseng

Abstract:

[Background] Bacterial soft rot poses a significant threat to plant roots, resulting in substantial agricultural losses. Our team identified Pseudomonas glycinae as the causative agent of bacterial soft rot in ginseng in 2023. [Objective] To delve into the genomic characteristics of P. glycinae XJFL-1, conduct a comparative genomics analysis for XJFL-1 with intra- and intergenus strains, and predict putative virulence factors and effectors of type II and III secretion systems (T2SS and T3SS, respectively). [Methods] We performed genome annotation, comparative genomics analysis, and gene family analysis to predict the genomic characteristics, genetic characteristics, and virulence genes. [Results] Genome annotation revealed the presence of genes encoding the enzymes involved in carbohydrate, amino acid, and protein metabolism, as well as key genes associated with flagellar movement, membrane biogenesis, and quorum sensing. Strain XJFL-1 was identified as P. glycinae based on ANI, dDDH, and collinearity analyses, and a high degree of intraspecific gene conservation was found for P. glycinae. Strain XJFL-1 encoded 37 plant cell wall-degrading enzymes (PCWDEs) including glycoside hydrolases (GHs), carbohydrate esterases (CEs), and polysaccharide lyases (PLs). In addition, the strain carried the genes encoding effectors of T2SS (e.g. lapA, lapB, lapC, phoA2, plcA, and cbpD) and T3SS (e.g. ipaH9.8, ipaH7.8, ipaH4.5, ipaH3, ipaH1.4, slrP, sspH2, sspH1, and NGR_a03640). However, pectinase genes were conspicuously absent. The results of the pectinase activity assay indicated that strain XJFL-1 was unable to secrete pectinase. [Conclusion] The results of comparative genomics and gene family analyses clarified the genetic relationship of strain XJFL-1 with representative strains of Pseudomonas and the intraspecific genetic characterization of P. glycinae. Additionally, the strain carried abundant genes encoding PCWDEs and effectors of T2SS and T3SS associated with pathogenicity.