RNA seq Analysis
RNA-seq expression analysis was performed using data from Hazzouri et al.’s study (Khaled M. Hazzouri et al., 2019). We used RNA-seq data of three or four replicates of varying days post-pollination ( 45,75,105,120 & 135 days ) in Kenezi ( dark brown color fruit) and Khalas ( light brown color fruit ) fruit. RNA-seq fastq files were downloaded from SRA ( PRJNA505138). The reads were aligned to the reference genome using STAR split read aligner ( V 2.7.1a) (Dobin et al., 2013) with t wo pass alignment. Thereafter, reads count per gene were calculated using the featureCounts program with the following parameter -p –countReadPairs -t exon -g gene_id -s 0’. Taking DESeq2 with the median-of-ratio method, read normalization was performed for the expression study.