Fig. 5.

Evolutionary origin of highly conserved de novo NMD_in exons. (A–D) Cross-species conservation of different categories of cassette exons under strong purifying selection in mammals is shown (A–C). Constitutive exons (D) are used as a control. In each panel, the heatmap indicates the conservation of each exon (rows) in each of the 60 vertebrate species (columns) ordered based on the phylogenetic tree (i.e., divergence from mouse, which is shown in the first column; placental mammals and nonmammalian vertebrates are underlined). A gray box in the heatmap indicates the presence of the exon in the species. Note that only exons with sequences conserved in mouse and human were included for the analysis. In A, exons from genes encoding RBPs or chromatin regulators are indicated on the right. (E) The percentage of conserved cassette exons across 60 vertebrate species. The phylogenetic tree of the species is shown on the top. The shaded species indicate the evolutionary period during which de novo NMD_in exons were created and finally fixed in mammals. (F) Median size of the introns flanking cassette exons under strong purifying selection pressure. Exons are grouped by their coding capacity. Error bars represent the robust estimate of the SEM.