Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach
Small RNAs (sRNAs) control a wide range of development and physiological pathways in plants. To address the response of sRNA biogenesis to drought stress, we identified sRNA biogenesis genes, including 11 encoding argonautes (AGO), 8 encoding Dicer-like proteins (DCL), and 9 encoding RNA-dependent R...
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2024-11-01
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| author | Mohammad Belal Charmaine Ntini Cherono Sylvia Misganaw Wassie Mahmoud Magdy Collins Ogutu Mohamed Ezzat Md Dulal Ali Mollah Yunpeng Cao Weihan Zhang Elsayed Nishawy Yuepeng Han |
| author_facet | Mohammad Belal Charmaine Ntini Cherono Sylvia Misganaw Wassie Mahmoud Magdy Collins Ogutu Mohamed Ezzat Md Dulal Ali Mollah Yunpeng Cao Weihan Zhang Elsayed Nishawy Yuepeng Han |
| author_sort | Mohammad Belal |
| collection | DOAJ |
| description | Small RNAs (sRNAs) control a wide range of development and physiological pathways in plants. To address the response of sRNA biogenesis to drought stress, we identified sRNA biogenesis genes, including 11 encoding argonautes (AGO), 8 encoding Dicer-like proteins (DCL), and 9 encoding RNA-dependent RNA polymerases (RDR) in the peach genome. Notably, the largest numbers of sRNA biogenesis genes are located to chromosome 1. The PAZ, PIWI, and MID domains were identified in PpAGOs, while the ribonuclease IIIa and IIIb domains were characterized in PpDCLs. The RDRP domain was recognized in PpRDRs. Orthologous similarity and collinearity analyses between Arabidopsis and peach revealed 5, 1, and 2 collinear blocks in AGOs, DCLs, and RDRs, respectively. Moreover, 41, 40, and 42 <i>cis</i>-acting elements were located in the promoters of <i>PpAGOs</i>, <i>PpDCLs</i>, and <i>PpRDRs</i>, respectively, with the majority related to drought stress response. Analysis of RNA sequencing (RNA-seq) data revealed that sRNA biogenesis genes were involved in drought stress response in different tissues. Furthermore, the expression of candidate genes was verified in two peach cultivars, Beijing 2-7 (BJ2-7) and Sinai (SN), which are tested as drought-tolerant and sensitive cultivars, respectively, based on the physiological and biochemical analyses, which revealed that the Chinese peach cultivar ‘BJ2-7’ exhibits greater drought resistance compared to the Egyptian peach cultivar ‘SN’. Interestingly, the expression of <i>PpAGO2b</i>, <i>PpDCL2b</i>, <i>PpDCL4</i>, and <i>PpRDR4</i> genes was induced in ‘BJ2-7’ but inhibited in ‘SN’ under drought stress. Overall, this study provides insight into the roles of sRNA biogenesis genes in response to drought stress in peach. |
| format | Article |
| id | doaj-art-cccc05e5f7c54b6baf290a052a9d5df8 |
| institution | OA Journals |
| issn | 2311-7524 |
| language | English |
| publishDate | 2024-11-01 |
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| series | Horticulturae |
| spelling | doaj-art-cccc05e5f7c54b6baf290a052a9d5df82025-08-20T01:54:01ZengMDPI AGHorticulturae2311-75242024-11-011011122810.3390/horticulturae10111228Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in PeachMohammad Belal0Charmaine Ntini1Cherono Sylvia2Misganaw Wassie3Mahmoud Magdy4Collins Ogutu5Mohamed Ezzat6Md Dulal Ali Mollah7Yunpeng Cao8Weihan Zhang9Elsayed Nishawy10Yuepeng Han11CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaUniversity of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, ChinaDepartment of Plant Biology, Faculty of Biology, Murcia University, 30100 Murcia, SpainFraunhofer Institute for Process Engineering and Packaging, IVV, 85354 Freising, GermanyCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, ChinaSmall RNAs (sRNAs) control a wide range of development and physiological pathways in plants. To address the response of sRNA biogenesis to drought stress, we identified sRNA biogenesis genes, including 11 encoding argonautes (AGO), 8 encoding Dicer-like proteins (DCL), and 9 encoding RNA-dependent RNA polymerases (RDR) in the peach genome. Notably, the largest numbers of sRNA biogenesis genes are located to chromosome 1. The PAZ, PIWI, and MID domains were identified in PpAGOs, while the ribonuclease IIIa and IIIb domains were characterized in PpDCLs. The RDRP domain was recognized in PpRDRs. Orthologous similarity and collinearity analyses between Arabidopsis and peach revealed 5, 1, and 2 collinear blocks in AGOs, DCLs, and RDRs, respectively. Moreover, 41, 40, and 42 <i>cis</i>-acting elements were located in the promoters of <i>PpAGOs</i>, <i>PpDCLs</i>, and <i>PpRDRs</i>, respectively, with the majority related to drought stress response. Analysis of RNA sequencing (RNA-seq) data revealed that sRNA biogenesis genes were involved in drought stress response in different tissues. Furthermore, the expression of candidate genes was verified in two peach cultivars, Beijing 2-7 (BJ2-7) and Sinai (SN), which are tested as drought-tolerant and sensitive cultivars, respectively, based on the physiological and biochemical analyses, which revealed that the Chinese peach cultivar ‘BJ2-7’ exhibits greater drought resistance compared to the Egyptian peach cultivar ‘SN’. Interestingly, the expression of <i>PpAGO2b</i>, <i>PpDCL2b</i>, <i>PpDCL4</i>, and <i>PpRDR4</i> genes was induced in ‘BJ2-7’ but inhibited in ‘SN’ under drought stress. Overall, this study provides insight into the roles of sRNA biogenesis genes in response to drought stress in peach.https://www.mdpi.com/2311-7524/10/11/1228<i>Prunus persica</i>droughtsmall RNAs<i>AGO</i><i>DCL</i><i>RDR</i> |
| spellingShingle | Mohammad Belal Charmaine Ntini Cherono Sylvia Misganaw Wassie Mahmoud Magdy Collins Ogutu Mohamed Ezzat Md Dulal Ali Mollah Yunpeng Cao Weihan Zhang Elsayed Nishawy Yuepeng Han Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach Horticulturae <i>Prunus persica</i> drought small RNAs <i>AGO</i> <i>DCL</i> <i>RDR</i> |
| title | Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach |
| title_full | Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach |
| title_fullStr | Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach |
| title_full_unstemmed | Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach |
| title_short | Genome-Wide Identification of <i>AGO</i>, <i>DCL</i>, and <i>RDR</i> Genes and Their Expression Analysis in Response to Drought Stress in Peach |
| title_sort | genome wide identification of i ago i i dcl i and i rdr i genes and their expression analysis in response to drought stress in peach |
| topic | <i>Prunus persica</i> drought small RNAs <i>AGO</i> <i>DCL</i> <i>RDR</i> |
| url | https://www.mdpi.com/2311-7524/10/11/1228 |
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