Fig. 2

The prevalent regulation of mRNA output by intron retention (IR) in V. dahliae. a Structure features of V. dahliae genes. The statistics of the length distribution of all introns (left) and exons (middle), as well as the exon composition of each gene are shown. RT-PCR validation of IR events detected by the current iRAS algorithm from both datasets (b); from the 2nd but not the 1st dataset (c); from the 1st but not the 2nd (d); from neither (e). We developed an algorithm to visualize the alternative splicing events in each gene. For each gene, cDNA reads mapped to unique genomic locations were plotted and numbered, and the type of alternative splicing and the dataset in which the AS was detected were indicated. One full example was shown in (b, left), and the IR containing region used for RT-PCR is detailed above the electrophoresis gel. To simplify the presentation and emphasizing the read layout in the AS region, we show the structure of the gene containing the AS event at the top diagram with the known exons being boxed in cyan, the intron in blue line and the UTR regions in purple boxes. The AS is enlarged below with the positions of PCR primers being indicated as black arrows, the nucleotide length composing the spliced products being numbered, and the alternative exons boxed in green. The black scale (horizontal axis) and numbers below indicated the genomic location. The sequence reads spanning the splice junctions are shown below the scale. The red and blue lines indicate the reads from V991b and V991w, respectively. For junction reads, the unmatched intronic region are shown in thinner green line; the fully aligned reads are shown below. In a few cases, the read layouts from both dataset are shown, with the results from the 1st dataset being boxed (c). A representative electrophoresis gel of the RT-PCR validation result corresponding to each pair of primers is shown. Two batches of total RNAs were used for RT-PCR validation; the loading order of V991b and V991w was different