Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa
Abstract Background The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-...
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07406-7 |
| _version_ | 1818622568146403328 |
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| author | Lan Yu Rongkai Guo Yeqin Jiang Xinghuo Ye Zhihong Yang Yijun Meng Chaogang Shao |
| author_facet | Lan Yu Rongkai Guo Yeqin Jiang Xinghuo Ye Zhihong Yang Yijun Meng Chaogang Shao |
| author_sort | Lan Yu |
| collection | DOAJ |
| description | Abstract Background The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. Results In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. Conclusions These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice. |
| first_indexed | 2024-12-16T18:27:14Z |
| format | Article |
| id | doaj.art-7c4bbe33d83f4298b52f500d4c3ad4bf |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-16T18:27:14Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7c4bbe33d83f4298b52f500d4c3ad4bf2022-12-21T22:21:22ZengBMCBMC Genomics1471-21642021-01-0122111410.1186/s12864-021-07406-7Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativaLan Yu0Rongkai Guo1Yeqin Jiang2Xinghuo Ye3Zhihong Yang4Yijun Meng5Chaogang Shao6College of Life Sciences, Huzhou UniversityShanghai Institute of Plant Physiology and Ecology, Chinese Academy of SciencesCollege of Life Sciences, Huzhou UniversityCollege of Life Sciences, Huzhou UniversityCollege of Life Sciences, Huzhou UniversityCollege of Life and Environmental Sciences, Hangzhou Normal UniversityCollege of Life Sciences, Huzhou UniversityAbstract Background The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. Results In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. Conclusions These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.https://doi.org/10.1186/s12864-021-07406-7Oryza sativaPhased small interfering RNAsPrecursorDegradome sequencingRegulatory network |
| spellingShingle | Lan Yu Rongkai Guo Yeqin Jiang Xinghuo Ye Zhihong Yang Yijun Meng Chaogang Shao Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa BMC Genomics Oryza sativa Phased small interfering RNAs Precursor Degradome sequencing Regulatory network |
| title | Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa |
| title_full | Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa |
| title_fullStr | Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa |
| title_full_unstemmed | Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa |
| title_short | Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa |
| title_sort | degradome sequencing based identification of phasirnas biogenesis pathways in oryza sativa |
| topic | Oryza sativa Phased small interfering RNAs Precursor Degradome sequencing Regulatory network |
| url | https://doi.org/10.1186/s12864-021-07406-7 |
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