Fig. 2

Alternative splicing of RNA processing genes occurs during germination. a Heatmap of the log ratios of isoform1/isoform2 for the 620 genes with at least two isoforms and average expression greater than 0.1 transcript per million (tpm). Only the genes that had a maximum isoform1/isoform2 ratio of > 2 and a minimum isoform1/isoform2 ratio of < 0.5 over the time course are shown. b Of the 620 genes displaying isoform variation, 612 were differentially expressed during germination. The proportion of these falling into the three clusters compared to the genome is shown (Cluster 1: increasing over time course, highest expression in seedling, Cluster 2: transiently peaking, Cluster 3: decreasing expression over time course with highest expression in seeds). c GO enrichment analysis showing the top three enriched categories. Examples of genes showing variations in isoform expression including (d) SR45, (e) PIF6 and (f) PhyB. The solid lines represent the average of three replicates