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 environm...
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BMC
2024-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11062-y |
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| author | Siyu Liu Xiong Lei Wenlong Gou Chunsen Xiong Wei Min Dandan Kong Xiaoyun Wang Tianqi Liu Yao Ling Xiao Ma Junming Zhao |
| author_facet | Siyu Liu Xiong Lei Wenlong Gou Chunsen Xiong Wei Min Dandan Kong Xiaoyun Wang Tianqi Liu Yao Ling Xiao Ma Junming Zhao |
| author_sort | Siyu Liu |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-5e8143dc90114d5594fd7529cc7092fc |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-5e8143dc90114d5594fd7529cc7092fc2024-12-01T12:11:19ZengBMCBMC Genomics1471-21642024-11-0125111710.1186/s12864-024-11062-yGenome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrassSiyu Liu0Xiong Lei1Wenlong Gou2Chunsen Xiong3Wei Min4Dandan Kong5Xiaoyun Wang6Tianqi Liu7Yao Ling8Xiao Ma9Junming Zhao10College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu Sichuan Academy of Grassland ScienceSchool of Life Science and Engineering, Southwest University of Science and TechnologyCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu Aba County Bureau of Science, Technology and Agriculture and Animal HusbandryCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 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.https://doi.org/10.1186/s12864-024-11062-yAGODCLRDRGene familyCentipedegrassAbiotic stresses |
| spellingShingle | Siyu Liu Xiong Lei Wenlong Gou Chunsen Xiong Wei Min Dandan Kong Xiaoyun Wang Tianqi Liu Yao Ling Xiao Ma Junming Zhao Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass BMC Genomics AGO DCL RDR Gene family Centipedegrass Abiotic stresses |
| title | Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass |
| title_full | Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass |
| title_fullStr | Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass |
| title_full_unstemmed | Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass |
| title_short | Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass |
| title_sort | genome wide identification characterization and expression analysis of key gene families in rna silencing in centipedegrass |
| topic | AGO DCL RDR Gene family Centipedegrass Abiotic stresses |
| url | https://doi.org/10.1186/s12864-024-11062-y |
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