Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice
Long non-coding RNAs (lncRNAs) play important roles in response to various biotic and abiotic stresses. So far, systematic identification and characterization of lncRNAs have been reported in a few model plant species and major crops, but their roles in abiotic stress response have not yet been repo...
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doaj-6f125b0a221048f2bd47ee3f7df11f5d2020-11-25T03:25:34ZengElsevierRice Science1672-63082020-01-012712131Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild RiceQi Weidong0Chen Hongping1Yang Zuozhen2Hu Biaolin3Luo Xiangdong4Ai Bing5Luo Yuan6Huang Yu7Xie Jiankun8Zhang Fantao9College of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaRice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, ChinaCipher Gene Limited Liability Company, Beijing 100080, ChinaRice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; Corresponding author.Long non-coding RNAs (lncRNAs) play important roles in response to various biotic and abiotic stresses. So far, systematic identification and characterization of lncRNAs have been reported in a few model plant species and major crops, but their roles in abiotic stress response have not yet been reported in common wild rice (Oryza rufipogon). Dongxiang wild rice (DXWR) possesses a high degree of drought resistance and has been well recognized as a precious genetic resource for drought resistant rice breeding. We presented the reference catalog of 1 655 novel lncRNA transcripts in DXWR using strand-specific RNA sequencing and bioinformatics approaches. Meanwhile, a total of 1 092 lncRNAs were determined as differentially expressed lncRNAs under drought stress. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which confirmed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. Furthermore, 8 711 transcripts were predicted as target genes of the differentially expressed lncRNAs. Functional annotation analysis based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases showed that the target genes were significantly enriched in cellular and metabolic processes, cell part, binding and plant hormone signal transduction, as well as many other terms related to abiotic stress resistance. These results expanded our understanding of lncRNA biology and provided candidate regulators for genetic improvement of drought resistance in rice cultivars. Keywords: Dongxiang wild rice, Drought stress, Long non-coding RNA, Systematic characterizationhttp://www.sciencedirect.com/science/article/pii/S1672630819301076 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Qi Weidong Chen Hongping Yang Zuozhen Hu Biaolin Luo Xiangdong Ai Bing Luo Yuan Huang Yu Xie Jiankun Zhang Fantao |
spellingShingle |
Qi Weidong Chen Hongping Yang Zuozhen Hu Biaolin Luo Xiangdong Ai Bing Luo Yuan Huang Yu Xie Jiankun Zhang Fantao Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice Rice Science |
author_facet |
Qi Weidong Chen Hongping Yang Zuozhen Hu Biaolin Luo Xiangdong Ai Bing Luo Yuan Huang Yu Xie Jiankun Zhang Fantao |
author_sort |
Qi Weidong |
title |
Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice |
title_short |
Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice |
title_full |
Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice |
title_fullStr |
Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice |
title_full_unstemmed |
Systematic Characterization of Long Non-Coding RNAs and Their Responses to Drought Stress in Dongxiang Wild Rice |
title_sort |
systematic characterization of long non-coding rnas and their responses to drought stress in dongxiang wild rice |
publisher |
Elsevier |
series |
Rice Science |
issn |
1672-6308 |
publishDate |
2020-01-01 |
description |
Long non-coding RNAs (lncRNAs) play important roles in response to various biotic and abiotic stresses. So far, systematic identification and characterization of lncRNAs have been reported in a few model plant species and major crops, but their roles in abiotic stress response have not yet been reported in common wild rice (Oryza rufipogon). Dongxiang wild rice (DXWR) possesses a high degree of drought resistance and has been well recognized as a precious genetic resource for drought resistant rice breeding. We presented the reference catalog of 1 655 novel lncRNA transcripts in DXWR using strand-specific RNA sequencing and bioinformatics approaches. Meanwhile, a total of 1 092 lncRNAs were determined as differentially expressed lncRNAs under drought stress. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which confirmed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. Furthermore, 8 711 transcripts were predicted as target genes of the differentially expressed lncRNAs. Functional annotation analysis based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases showed that the target genes were significantly enriched in cellular and metabolic processes, cell part, binding and plant hormone signal transduction, as well as many other terms related to abiotic stress resistance. These results expanded our understanding of lncRNA biology and provided candidate regulators for genetic improvement of drought resistance in rice cultivars. Keywords: Dongxiang wild rice, Drought stress, Long non-coding RNA, Systematic characterization |
url |
http://www.sciencedirect.com/science/article/pii/S1672630819301076 |
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