Pan-genome analysis of Ralstonia solanaceaum associated with tobacco bacterial (PRJCA042701)
Tobacco bacterial wilt, caused by Ralstonia solanacearum, poses a significant threat to tobacco production in most major tobacco-growing regions of China. Pangenomic function of R. solanaceaum associated with tobacco bacterial wilt in China has not been explored. Here, 204 strains of R. solanacearum were isolated from infected tobacco plants across 12 provinces and autonomous regions in China. Molecular identification and biovar typing of the R. solanacearum strains revealed all the isolates were found in phylotype I and biovar III. Seven sequevars were identified and sequevar 15 was the most prevalent. Pathogenicity tests indicated that the strong pathotype represented 29% of the strains, and was found in the southwest tobacco-growing region of China. Notably, significant pathogenic variation was observed within strains of the same sequevar, and no clear correlation was found between the sequevar type and pathogenicity. Using Oxford Nanopore sequencing, we analyzed 103 strains of tobacco R. solanacearum from different geographical origins and pathotypes. The pangenome of R. solanacearum is comprised of 9008 non-redundant genes, divided into a core genome (36%), accessory genome (48.7%) and isolate-specific genes (15%). Core genome functions were related to oxidation-reduction reaction process and DNA transcription regulation, while the accessory genome was linked to DNA recombination, integration, and transposition. SNP analysis revealed an average of 36,740 SNP loci per strain, indicating evolutionary purification with ka/ks value below 1. Phylogenetic analysis divided 99 strains into 4 main groups, with sequevars correlated to specific branches, reflecting evolutionary relationships. We identified 2226 genomic islands across the strains, with each strain containing 18-25 islands, primarily related to translation regulation, transposition, and transposase activity. Analysis of virulence factors using the virulence factors database (VFDB) highlighted 1252 virulence genes within these islands, with a significant portion (36.5%) linked to effector transport systems, predominantly the type III secretion system (66.7%). Each strain averaged 60 type III effector proteins, with RipBK and RipAZ2 unique to highly pathogenic strains. This study provides a comprehensive understanding of pan-genome of R. solanacearum causing tobacco bacterial wilt in China, facilitating valuable insights into molecular variation and establishing a basis for disease control.