Fig. 4

Variety-specific AS events associated with the gain or loss of a splice site. For each event, the arrow indicates the position of the SNP involved in the gain or loss of a splice site, by reference to the canonical GT (5′-donor) -and AG (3′-acceptor) sequences. The Sashimi plots showing RNAseq reads aligned to gene annotations are respectively color-coded in red for Gw and blue for Ri. The transcript variants included in the VCost.v3 genome annotation are presented as dark blue exon-plots: exons as solid lines and introns as dashed lines. The table under each plot summarizes, from top to bottom, first line: the gene ID, the region affected (3′-UTR, 5′-UTR orCDS), and the genomic location of the SNP, in brackets; second line: the nucelotide sequence at the position of the splice site in each variety (the specific nucleotide is in bold red font); third line: the splice site modification linked to the SNP and the specific alternative isoform (or specific event) produced