Dual RNA-seq Reveals the Global Transcriptome Dynamics of and Pepper () Hypocotyls During Bacterial Wilt Pathogenesis.

Bacterial wilt, caused by , 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 pathogenesis. We assembled the complete genome of strain Rs-SY1 and identified 5,106 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 postinoculation (dpi) with Dual RNA-seq was used to simultaneously capture transcriptome changes in the host and pathogen at 3 and 7 dpi. A total of 1,400, 3,335, 2,878, and 4,484 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 . When comparing in planta and nutrient agar growth of the , 218 and 1,042 DEGs of (RDEGs) were detected at 3 and 7 dpi, respectively. Additional analysis of the RDEGs suggested that enhanced starch and sucrose metabolism, and upregulation of virulence factors may promote colonization. Strikingly, 26 genes were found to have similar DEG patterns during a variety of host- interactions. This study provides a foundation for a better understanding of the transcriptional changes during pepper- interactions and will aid in the discovery of potential susceptibility and virulence factors.