(A) A PATC density analysis for SET-25 and SET-32-dependent endo-siRNAs gene targets. The PATC density values (obtained from Frøkjær-Jensen et al., 2016) are presented for all protein-coding genes, gene targets of endo-siRNAs that depend on SET-25 or SET-32 and gene targets of endo-siRNAs associated with WAGO small RNA pathways (HRDE-1,WAGO-1 or ERGO-1). **p-value<0.005, *p-value<0.05, Wilcoxon rank sum test. For clarity of display, values are shown in log2 scale (after addition of 1). The median (black line) and average levels (numbers) of PATC density levels of each plot are indicated (log2 scale). (B) An enrichment analysis of genes conserved at different levels and duplicated genes amongst gene targets of SET-25- and SET-32-dependent endo-siRNAs. The gene sets were generated based on the homology field in WormBase that details the orthologs and paralogs of each nematode gene. We defined a duplicated gene as a gene that has a paralog in C. elegans. We define genes unique to C. elegans as genes that lack an ortholog amongst the nematode species we examined (see Materials and methods). For statistical analysis, control enrichment values were obtained from 10,000 random gene sets with the same size as the examined endo-siRNA-target gene list. ****p-value<0.0001,***p-value<0.001, *p-value<0.05 (C) An analysis of endo-siRNAs fold changes in rnp-2 mutants for genes targets of endo-siRNAs downregulated or upregulated in set-25 mutants or all genes. All p-values<0.001, Wilcoxon rank sum test. (D) An analysis of intron numbers of gene targets of SET-25- and SET-32-dependent endo-siRNAs and WAGO-associated endo-siRNAs compared to all protein-coding genes. In cases of genes that have more than one transcript, the average intron value is used. The median intron number of each plot is indicated (log2 scale). ***p-value<0.001,**p-value<0.005, Wilcoxon rank sum test. (E) An analysis of splicing motif divergence score (based on Newman et al., 2018) of gene targets of SET-25 and SET-32-dependent endo-siRNAs, WAGO associated endo-siRNAs and all protein-coding genes. The median score levels of each plot are indicated. p-value>0.05, Wilcoxon rank sum test.