RNA sequencing (RNA-Seq)

Several studies of powdery mildew pathogen induced genes in host plants have found the highest number of differentially expressed genes in later time points (Li et al., 2016; Li, Dong, et al., 2019; Polonio et al., 2019). The qPCR results revealed that gene expression of the marker genes showed elevated levels in time point 72 h post inoculation (hpi; Supplementary Figure 1). Hence, we selected samples from time point 72 hpi for RNA sequencing. The samples were sequenced using Illumina NextSeq 500 platform in the Institute of Biotechnology of the University of Helsinki using paired end sequencing. The length of the forward reads was 78 and reverse reads 74 bases. The sequenced reads were first trimmed and low quality reads were removed using Trimmomatic software (Bolger, Lohse, & Usadel, 2014), resulting in an average library size of 14.6 million reads.