(A) Gene plot diagram showing reads mapping to unc-54(e1092), with position of e1092 early stop codon indicated. Read counts are averaged over the entire sequence overlapping a read (not just the 5’end). All data in this figure were in the skih-2(cc2854) pelo-1(cc2849) double mutant background, abbreviated skih-2 pelo-1. (B) Zoom in of region upstream of e1092. Reads are displayed according to where their 5’ends map. (C) Genome-wide counts of Ribo-seq reads with and without smg-1(e1228), with indicated genes highlighted. ‘Endog. SKI/PELO’ are the same genes identified in Figure 4A. (D) Genome-wide distribution of 15-18nt Ribo-seq reads with and without smg-1(e1228). Solid lines are all genes, and dotted lines are endogenous SKI/PELO targets, as identified in Figure 4A. Purple is the smg-1(+) strain, black is smg-1(e1228). (E) X-axis shows the total number of 15-18nt Ribo-seq reads in a skih-2/pelo-1 double mutant with and without smg-1(e1228). Y-axis shows the fraction of those reads that come from the smg-1(e1228) mutant. Endogenous SKI/PELO targets are highlighted (red), and endogenous SKI/PELO targets with >95% of 15-18nt Ribo-seq reads derived from the smg-1(+) strain are highlighted in orange. (F) Log2 fold change in total mRNA levels as assayed by RNA-seq for genes shown in Figure 1E, using published datasets from Muir et al., 2018. Genes highlighted in blue are the 12 endogenous NMD targets identified in (Barberan-Soler et al., 2009) and described in the text. p-Value from Kolmogorov–Smirnov test relative to all genes (black line). (G) Distribution of 15-18nt Ribo-seq reads at xbp-1 locus with and without smg-1(e1228). (H) Brood size of skih-2(cc2854) pelo-1(cc2849) with and without smg-1(e1228). Brood size analysis performed as in Figure 2D and described in Materials and methods. p-Value from Mann Whitney U test. The skih-2/pelo-1 double mutant was backcrossed to the smg-1(e1228) background as a control, and smg-1(+) homozygotes made by segregating away the smg-1(e1228) allele.