RNA-seq Analysis of Capsicum Cultivar

The TransZol kit (TransGen Biotech, Inc., Beijing, China) was used to extract total RNA, and HiScript^®ⅡQRT SuperMix for qPCR (+gDNA wiper) vazyme kit (Vazyme, Piscataway, NJ, United States) was used to synthesize the reverse cDNA. The raw data for the RNA-seq analysis were downloaded from Pepper Hub (Liu et al., 2017 (link)), and a high-generation inbred capsicum line “6421”, was used. Fastqc was used for quality control of the sequencing data (Brown et al., 2017 (link)) and the low-quality sequences were removed using Trimmmatic-0.36 (Bolger et al., 2014 (link)). HISAT2 was used to align the sequencing reads to the reference genome, “Zunla” (Kim et al., 2014 (link)), and FeatureCounts was used to calculate the number of counts (Liao et al., 2014 (link)). Standardize counts data from DESeq2 package in R (Varet et al., 2016 (link)), and the fragments per kilobase of exon model per million mapped reads (FPKM) value represented the corresponding gene expression.