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

doi:10.1186/s12864-021-07754-4

	Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
	Xu, Yong-Chao ; Zhang, Jie ; Zhang, Dong-Yan ; Nan, Ying-Hui ; Ge, Song; Guo, Ya-Long
	2021
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	22 期号:1
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.
关键词	Drought stress Long noncoding RNA O nivara Strand-specific RNA-seq Wild rice
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/s12864-021-07754-4
收录类别	SCI
语种	英语
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)
WOS记录号	WOS:000662813500003
出版者	BMC
文献子类	Article
出版地	LONDON
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
作者邮箱	yalong.guo@ibcas.ac.cn
作品OA属性	Green Published, gold, Green Submitted
引用统计	被引频次：13[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/26552
专题	系统与进化植物学国家重点实验室
作者单位	1.[Xu, Yong-Chao 2.Zhang, Jie 3.Zhang, Dong-Yan 4.Nan, Ying-Hui 5.Ge, Song 6.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 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).

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