Genome-Wide Identification of the Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Cucumber (Cucumis sativus L.)

Dicer, Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) comprise the core components of RNA-induced silencing complexes, which trigger RNA silencing. Here, we performed a complete analysis of the cucumber Dicer-like, AGO, and RDR gene families including the gene structure, genomic localization, and phylogenetic relationships among family members. We identified seven CsAGO genes, five CsDCL genes, and eight CsRDR genes in cucumber. Based on phylogenetic analysis, each of these genes families was categorized into three or four clades. The orthologs of CsAGOs, CsDCLs, and CsRDRs were identified in apple, peach, wild strawberry, foxtail millet, and maize, and the evolutionary relationships among the orthologous gene pairs were investigated. We also investigated the expression levels of CsAGOs, CsDCLs, and CsRDRs in various cucumber tissues. All CsAGOs were relatively higher upregulated in leaves and tendrils than in other organs, especially CsAGO1c, CsAGO1d, and CsAGO7. All CsDCL genes were relatively higher upregulated in tendrils, with almost no expression detected for CsDCL1, CsDCL4a, or CsDCL4b in other organs. In addition, CsRDR1a, CsRDR2, CsRDR3, and CsRDR6 had relatively higher upregulation in tendrils, whereas almost all CsRDRs were downregulation in other organs. The results of this study will facilitate further studies of gene silencing pathways in cucumber.