Comparative genome analysis of two peanut Ralstonia solanacearum strains with significant difference in pathogenicity reveals 16S rRNA dimethyltransferase RsmA involved in inducing immunity

Bacterial wilt disease, caused by Ralstonia solanacearum, seriously threaten the quality and yield of peanut (Arachis hypogaea L.). Identification of proteins inducing host immune response in R. solanacearum is an important way towards exploring resistance genes in peanut. In previous study, we found that the pathogenicity was significant different between peanut R. solanacearum ZKRS126 and ZKRS146. In this study, comparative genomics analysis was performed to reveal the difference of the genomes between ZKRS126 and ZKRS146, as well as the function of the strain specific gene rsmA in triggering immunity. Compared with ZKRS146, ZKRS126 caused less cell death in the peanut leaves and its proliferation and pathogenicity were significantly attenuated. Whole genome sequencing revealed that the genomes of ZKRS126 and ZKRS146 were composed of one chromosome, one megaplasmid and one small plasmid. The genome size of ZKRS126 (6,059,912 bp) was slightly larger than that of ZKRS146 (6,053,081 bp). Comparative genomics analysis showed that the genetic relationship between ZKRS126 and ZKRS146 was very close. In both ZKRS126 and ZKRS146, 73 Type III secretion system-secreted effectors (T3Es) were identified by retrieving the effector repertoire, respectively. The gene sequences of T3Es were identical between ZKRS126 and ZKRS146. Comparing all the coding genes between ZKRS126 and ZKRS146, 42 specific genes were identified in ZKRS126 and 43 in ZKRS146. Loss of the specific gene rsmA in ZKRS126 resulted in more virulence, and complementarity of rsmA in mutant strains recovered hypovirulence. The cAMP assay demonstrated RsmA was not a T3E. In Nicotiania benthamiana leaves, transient expression of rsmA significantly induced the up-regulated expression of marker genes in HR, PTI, SA, and JA pathways, indicating RsmA might trigger the plant immunity by activating the immune-related pathways. This study not only obtained the complete genomes of two peanut R. solanacearum strains, but also revealed their differences in the genome levels through comparing analysis. The function verification of RsmA provided the way for the identification of immunity elicitors, which will accelerate the breeding of bacterial wilt-resistant peanut varieties in the future.