Figure 5

Comparison of alternative splicing between the wild-type and SAD1-OE plants. (A) Profiling the normalized (by total uniquely mapped reads) read coverage of the splice junctions that were over-represented in the sad1 mutant relative to the wild type and SAD1-OE. The profiles indicate that the AS patterns in sad1 were completely or largely restored by overexpressing SAD1. (B) The counts of each type of AS event in the wild type and SAD1-OE. The green/blue bars represent forward and reverse sequencing reads. (C) The total counts of the splice junction reads from each type of AS in the wild type and SAD1-OE. The P values were calculated by Fisher’s exact test comparing the junction read counts and the uniquely mapped reads between the wild type and SAD1-OE. (D) The sequences around the alternative 5′SSs and 3′SSs that were absent in the SAD1-OE were shown by Weblogo. (E) Distribution of activated alternative 5′SSs and 3′SSs around the dominant ones are shown. These alternative 5′SSs and 3′SSs were enriched in the downstream or upstream 10 bp region of the dominant 5′SSs and 3′SSs (position 0 on the x-axis), respectively. (F) Profiling the normalized (by total uniquely mapped reads) read coverage of the introns that were over-represented in the sad1 mutant relative to the wild type and SAD1-OE. The profiles indicate that the intron retention in sad1 was largely restored by overexpressing SAD1. AS, alternative splice; sad1, sad1 mutant; SAD1-OE, plants over-expressing wild-type SAD1 in the sad1 mutant background; WT, wild type.