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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

文献类型：期刊论文

作者Xu, Yong-Chao; Zhang, Jie; Zhang, Dong-Yan; Nan, Ying-Hui; Ge, Song; Guo, Ya-Long
刊名BMC GENOMICS
出版日期2021
卷号22期号:1
关键词Drought stress Long noncoding RNA O nivara Strand-specific RNA-seq Wild rice
ISSN号1471-2164
DOI10.1186/s12864-021-07754-4
文献子类Article
英文摘要BackgroundWild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown.ResultsHere, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding-noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding-noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding-noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare.ConclusionWe identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.
学科主题Biotechnology & Applied Microbiology ; Genetics & Heredity
出版地LONDON
WOS关键词SEQ REVEALS WIDESPREAD ; GENOME-WIDE ANALYSIS ; RNA ; TOLERANCE ; GENE ; RESISTANCE ; CHROMATIN ; NUMBER
WOS研究方向Science Citation Index Expanded (SCI-EXPANDED)
语种英语
WOS记录号WOS:000662813500003
出版者BMC
资助机构National Natural Science Foundation of China [31925004] ; Strategic Priority Research Program of the Chinese Academy of Sciences [XDB27010305, XDA08020103] ; China Postdoctoral Science Foundation [2020 M680749] ; Innovative Academy of Seed Design, Chinese Academy of Sciences
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/26552]  
专题植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文
作者单位1.Nan, Ying-Hui
2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
3.Ge, Song
4.Zhang, Dong-Yan
5.Zhang, Jie
6.[Xu, Yong-Chao
7.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式
GB/T 7714		 Xu, Yong-Chao,Zhang, Jie,Zhang, Dong-Yan,et al. Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)[J]. BMC GENOMICS,2021,22(1).
APA Xu, Yong-Chao,Zhang, Jie,Zhang, Dong-Yan,Nan, Ying-Hui,Ge, Song,&Guo, Ya-Long.(2021).Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara).BMC GENOMICS,22(1).
MLA Xu, Yong-Chao,et al."Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)".BMC GENOMICS 22.1(2021).

入库方式： OAI收割

来源：植物研究所

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