Fig. 2

Various alternate splicing (AS) events and their distribution patterns in different virus treatments. (a) Representation of various AS events frequently observed in P. vulgaris. (b) Number of genes and corresponding transcripts with significant (padj < 0.05) differential splicing (AS) patterns for each virus treatments. (c) Different in number of different AS forms (significantly spliced transcripts) in healthy and NL1-I infected samples. (d) Different in number of different AS forms (significantly spliced transcripts) in healthy and BCMV-S2 infected samples. The transcripts were built using cufflinks2 and significant differential splicing events were detected using cuffdiff2 [36, 37]. Low abundance transcripts (FPKM < 0.3) were eliminated to avoid misassembly issues due to low read count. Alternate Splicing Transcriptional Landscape Visualization Tool, ASTALAVISTA [38], was used to characterize different AS events