Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass

Abstract

Background Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) are essential components of RNA silencing pathways in plants. These components are crucial for the generation and regulatory functions of small RNAs, especially in plant development and response to environmental stresses. Despite their well-characterized functions in other plant species, there is limited information about these genes and their stress responses in centipedegrass ( Eremochloa ophiuroides ), a key turfgrass species. Results Using genome-wide analysis we identified 20 AGO , 6 DCL , and 10 RDR members in centipedegrass and provided a comprehensive overview of their characteristics. We performed the chromosomal location, gene duplication, syntenic analysis, conserve motif, gene structure, and cis -acting elements analysis. And conducted phylogenetic analyses to clarify the evolutionary relationships among the EoAGO , EoDCL , and EoRDR gene families. Three-dimensional modeling prediction of EoAGO, EoDCL, and EoRDR proteins supported the phylogenetic classification. Furthermore, we examined the expression patterns of these genes in different tissues (spike, stem, leaf, root, and flower) and under different stress conditions (cold, salt, drought, aluminum, and herbicide) using RT-qPCR. The results revealed that most of EoAGO , EoDCL , and EoRDR genes were upregulated in response to multiple abiotic stresses, while some exhibited unique responses, suggesting potential specialized regulatory functions. Conclusion In this study, we performed a comprehensive genome‑wide identification, and phylogenetic and expression pattern analyses of the EoAGO , EoDCL and EoRDR gene families. Our analysis provides a foundation for future research on the RNA silence elements of turfgrass, and affords scientific basis and insights for clarifying the expression patterns of EoAGO , EoDCL and EoRDR genes under adversity stress. Further functional validation and molecular breeding of these genes can be carried out for enhancing the stress resistance of centipedegrass. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-11062-y.