Fig. 5

Expression of genes belonging to the Wx cluster. a Representation of the Wx cluster and Bar-plots indicating the mean expression values, corresponding to the number of reads mapping at each locus on rice reference genome (raw read counts as obtained from DESeq-normalized matrix of expression data), of the three biological replicates (y-axis) for each cv (ARB–Arborio, BAL–Balilla, CAR–Carnaroli, GV–Gigante Vercelli, VN–Vialone Nano and VOL–Volano; x-axis). b Sashimi plots of RNA-Seq reads aligned at LOC_Os06g04200, on Nipponbare Reference Genome, in the six different varieties. Only one biological replicate for each genotype is represented. The alignments were performed using the IGV software. The coverage for each alignment track is plotted as a bar graph. Coverage ranges for each variety are reported in the bars on the left. Arcs represent splice junctions. Junction depth is indicated by the number in the arc and the thickness of the arc. Graphs were built setting a Min Junction Coverage corresponding to the 1 % of the mean exons coverage. The alternative isoforms of the gene annotated in the Rice Genome browser MSU database are reported in the lower bar. Thick and intermediate boxes represent exons and 5’ and 3’-UTR regions, respectively. Lines between boxes indicate introns. The mapping coverage for each variety at the level of each exon and intron is represented by the coloured parts