Fig. 1

Promoter usage across the O. dioica life cycle. a The 6-day life cycle with stages used for single-nucleotide resolution of TSS-mapping by CAGE are labelled (oocyte, tailbud, tadpole, day 2, female day 6 and male day 6). Changes in the proportion of mRNAs that are trans-spliced (blue) and non-trans-spliced (pink) are shown schematically in the upper panel, above a colour bar indicating major promoter categories (colours corresponding to clusters in (b)). Developmental stages are shown schematically below this bar. b Expression profiles obtained from self-organising map clustering of CAGE TSSs (CTSSs). Each beanplot shows the distribution of relative expression (y-axis) originating at CTSSs (number of CTSSs above each plot) within each cluster at each developmental stage (x-axis) labelled only in the bottom right plot. Coloured boxes and associated labels indicate groups of clusters with similar expression profiles. c Beanplots showing the distribution of interquantile widths of tag clusters (TCs) within each stage and assigned to the expression cluster of the dominant CTSS (plots are ordered and coloured as in (b)) revealing an increase in the use of sharp promoters in adult(tissue)-specific genes. d Heatmap showing the number of promoters that shift up- or down-stream in location between all possible pairs of developmental stages. The highest number of shifting promoters occurs between pre-metamorphic (tailbud) and post-metamorphic (day 2 and day 6) stages. e Distribution of the interquartile widths of consensus promoter regions of trans-spliced (SL) and non-trans-spliced (Non-SL) genes