Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii

RNA silencing regulates diverse cellular processes in plants. Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) proteins are core components of RNA interference (RNAi). Despite their functional significance, the systematic identification and characterization of these families have remained largely unexplored in <i>Siraitia grosvenorii</i>. Using HMMER and Pfam analyses, we identified six <i>SgAGO</i>, four <i>SgDCL</i>, and six <i>SgRDR</i> genes. Phylogenetic analysis classified SgAGOs, SgDCLs, and SgRDRs into five, four, and four clades, respectively, all of which clustered closely with homologs from other <i>Cucurbitaceae</i> species, demonstrating lineage-specific evolutionary conservation. Promoter <i>cis</i>-element analysis revealed the significant enrichment of hormonal (methyl jasmonate, abscisic acid) and stress-responsive (light, hypoxia) elements, indicating their roles in environmental adaptation. Tissue-specific expression profiling showed that most <i>SgAGO</i>, <i>SgDCL</i>, and <i>SgRDR</i> genes were highly expressed in flowers and mid-stage fruits (35 days after pollination), while <i>SgAGO10.1</i> exhibited stem-specific expression. By contrast, <i>SgRDR1.2</i> displayed no tissue specificity. Notably, sex-biased expression patterns in dioecious flowers suggested the RNAi-mediated regulation of gametophyte development and their potential roles in reproductive and secondary metabolic processes. This study lays the foundation for further exploration of RNAi machinery's role in coordinating mogroside biosynthesis and stress resilience in <i>S. grosvenorii</i> while providing potential targets for genetic improvement.