Fig. 5

The transcriptome landscape under heat stress. The expression pattern of dispersed duplicated genes under treatments comparing 26°C against 20°C at St phase, shown for homologous sequence sets that contain a two and b three copies, in three possible outcomes: upregulated (+), downregulated (−), and not significant (·). c Proportion of dispersed DEGs that share similar expression pattern in homologous sets containing ≥ 3 of such copies. d Heatmap and clusters of gene expression pattern across triplicate samples at 20, 26, and 30°C in the St phase, showing eight superclusters (SCs). Centered log₂(FPKM + 1) values are shown. e Post-transcriptional regulation in P. cordatum, shown for 4550 genes in distinct duplication modes (counter-clockwise): dispersed, tandem, proximal, and singleton. Features shown from the inner-most to the outer-most circle: differential exon usage (blue), differential editing of mRNA per gene in response to growth phase (green/brown), and differential mRNA editing per gene in response to temperature (red/purple). In each circle, a bar in a light shade indicates the number of corresponding features identified in a gene, a bar in a dark shade indicates the number of statistically significant features in a gene. The bottom-left legend shows the distinct scenarios for identifying sites for mRNA editing in all transcripts versus differentially edited sites