Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
Abstract RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), an...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-30827-1 |
| _version_ | 1827984772472766464 |
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| author | Shiyu Yun Xin Zhang |
| author_facet | Shiyu Yun Xin Zhang |
| author_sort | Shiyu Yun |
| collection | DOAJ |
| description | Abstract RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant. |
| first_indexed | 2024-04-09T23:02:58Z |
| format | Article |
| id | doaj.art-7ccaf3f8674f49e5bc27a1c46f74e4b1 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T23:02:58Z |
| publishDate | 2023-03-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj.art-7ccaf3f8674f49e5bc27a1c46f74e4b12023-03-22T10:51:15ZengNature PortfolioScientific Reports2045-23222023-03-0113111510.1038/s41598-023-30827-1Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoaShiyu Yun0Xin Zhang1Institute of Industrial Crops, Shanxi Agricultural UniversityInstitute of Industrial Crops, Shanxi Agricultural UniversityAbstract RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant.https://doi.org/10.1038/s41598-023-30827-1 |
| spellingShingle | Shiyu Yun Xin Zhang Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa Scientific Reports |
| title | Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa |
| title_full | Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa |
| title_fullStr | Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa |
| title_full_unstemmed | Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa |
| title_short | Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa |
| title_sort | genome wide identification characterization and expression analysis of ago dcl and rdr families in chenopodium quinoa |
| url | https://doi.org/10.1038/s41598-023-30827-1 |
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