Dual RNA-seq reveals the global transcriptome dynamics of Ralstonia solanacearum and pepper (Capsicum annuum) hypocotyls during bacterial wilt pathogenesis.

Bacterial wilt, caused by Ralstonia solanacearum (Rso), is a serious disease in pepper. However, the interaction between the pathogen and pepper remains largely unknown. This study aimed to gain insights into determinants of pepper susceptibility and Rso pathogenesis. We assembled the complete genome of Rso strain Rs-SY1 and identified 5106 predicted genes, including 84 type III effectors (T3E). RNA-seq was used to identify differentially expressed genes (DEGs) in susceptible pepper CM334 at 1- and 5-days post-inoculation (dpi) with Rso, and dual RNA-seq was used to simultaneously capture transcriptome changes in the host and pathogen at 3 and 7 dpi. A total of 1400, 3335, 2878, and 4484 DEGs of pepper (PDEGs) were identified in the CM334 hypocotyls at 1, 3, 5, and 7 dpi, respectively. Functional enrichment of the PDEGs suggests that inducing ethylene production, suppression of photosynthesis, downregulation of polysaccharide metabolism, and weakening of cell wall defenses may contribute to successful infection by Rso. When comparing in planta and nutrient agar growth of the Rso, 218 and 1042 DEGs of Rso (RDEGs) were detected at 3 and 7 dpi, respectively. Further analysis of the RDEGs suggested that enhanced starch and sucrose metabolism, and upregulation of virulence factors may promote Rso colonization. Strikingly, 26 Rso genes were found to have similar DEG patterns during a variety of host-Rso interactions. This study provides a foundation for a better understanding of the transcriptional changes during pepper-Rso interactions and will aid in the discovery of potential susceptibility and virulence factors.