Identification and analysis of RNA interference-related enzyme gene families in Setaria italica

Dicers, argonautes, and RNA-dependent RNA polymerases (RDRs) are core and important components in RNA interference (RNAi) pathways, but there is no systematic report about them in Setaria italica (foxtail millet). In order to elucidate the characteristics of these genes related to RNA interference in foxtail millet, this study undertook a complete analysis of these gene families in S. italica, which included protein physical and chemical properties, prediction of subcellular location, protein conservative motif analysis, gene conserved domains, phylogenetic relatedness, and transcriptome expression profiling. A total of 24 RNA interference-related enzyme genes were identified. The group contained 7 dicers, 13 argonautes, and 4 RDRs. The phylogenetic tree analysis revealed that these genes cluster into three clades. Genes in the same clades have common conserved domains. Although most of the genes can be expressed simultaneously in leaves, stems, and panicles at six different development stages, the expression is most significant during the different development stages of the panicles and stem. This study provides a theoretical basis for further studies, and improves understanding about the function of epigenetic modification during the reproduction and development of S. italica.