The PRINSEQ-lite software (version 0.20.4) was used (63) to trim and filter raw reads. Reads longer than 30 bp, together with a minimum quality score of >15, were used for subsequent analyses. The Pairfq script was used for separation of paired and single reads. Clean reads were mapped to the C. elegans genome using HISAT2 (version 2.0.5) (64) with default parameters. The number of mapped reads was counted by featureCounts (version 1.5.0) (65). Differential gene expression analysis was performed using the DESeq2 package (66). An adjusted P value ≤ 0.05 was used as the threshold to identify the differentially expressed genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for the differentially expressed genes were conducted using the Cytoscape plugins BiNGO (67) and ClueGO (68), respectively. Plots for the mapped reads were generated by igvtools (69). The accession numbers for the hir-1 samples are SRX3564686, SRX3564687, and SRX3564688; the accession numbers for the controls are SRX3563003, SRX3563021, and SRX3563026—all under the Sequence Read Archive (SRA) BioProject PRJNA430003.

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