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

Content Provider	Springer Nature : BioMed Central
Author	Liu, Siyu Lei, Xiong Gou, Wenlong Xiong, Chunsen Min, Wei Kong, Dandan Wang, Xiaoyun Liu, Tianqi Ling, Yao Ma, Xiao Zhao, Junming
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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-11062-y.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-11062-y
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-11-26
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics AGO DCL RDR Gene family Centipedegrass Abiotic stresses
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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