Dual RNA-Sequencing of chili pepper cultivars and Xanthomonas euvesicatoria pv. euvesicatoria causing bacterial leaf spot (BLS)

Chili pepper (Capsicum annum) is a globally important crop, but its production is impacted by Bacterial Leaf Spot (BLS) disease, caused by Xanthomonas euvesicatoria pv. euvesicatoria. The fine-scale interaction between the pathogen and host remains unknown. Utilising stranded total RNA sequencing and the Illumina NovaSeq6000, high-depth Dual RNA-Sequencing was undertaken to investigate the host and pathogen gene expression profiles for a resistant and a susceptible cultivar over a time course of 0, 7 and 14 days after infection. A customised host-pathogen tailored ribosomal RNA (rRNA) depletion step removed >95% rRNA in all samples. Remaining sequences were mapped into host (65-85%) and pathogen (0.01-8.9%) genomes. Differentially expressed genes (DEGs) were identified using fold change in expression and Manhattan distance of each treatment, compared to controls.