Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change

doi:10.1016/j.molp.2017.04.007

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change
	Xu, Qin 6; Song, Zhihong 1,6; Zhu, Caiyun 1,5; Tao, Chengcheng 1,6; Kang, Lifang 6; Liu, Wei 5; He, Fei 4; Yan, Juan 3; Sang, Tao 5,6
刊名	BMC PLANT BIOLOGY
	2017
卷号	17
关键词	Population transcriptome lncRNAs Miscanthus lutarioriparius Co expression Environmental response Expression diversity
ISSN号	1471-2229
DOI	10.1016/j.molp.2017.04.007
文献子类	Article
英文摘要	Background: Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change are still poorly understood. Here we identified 17,610 lncRNAs and calculated their expression levels based on RNA-seq of 80 individuals of Miscanthus lutarioriparius from two environments, the nearly native habitats and transplanted field, respectively. Results: LncRNAs had significantly higher expression diversity and lower expression frequency in population than protein coding mRNAs in both environments, which suggested that lncRNAs may experience more relaxed selection or divergent evolution in population compared with protein coding RNAs. In addition, the increase of expression diversity for lncRNAs was always significantly higher and the magnitude of fold change of expression in new stress environment was significantly larger than protein-coding mRNAs. These results suggested that lncRNAs may be more sensitive to environmental change than protein-coding mRNAs. Analysis of environment-robust and environment-specific lncRNA-mRNA co-expression network between two environments revealed the characterization of lncRNAs in response to environmental change. Furthermore, candidate lncRNAs contributing to water use efficiency (WUE) identified based on the WUE-lncRNA-mRNA co-expression network suggested the roles of lncRNAs in response to environmental change. Conclusion: Our study provided a comprehensive understanding of expression characterization of lncRNAs in population for M. lutarioriparius under field condition, which would be useful to explore the roles of lncRNAs and could accelerate the process of adaptation in new environment for many plants.
学科主题	Biochemistry & Molecular Biology ; Plant Sciences
出版地	LONDON
WOS关键词	LONG NONCODING RNAS ; MISCANTHUS ENERGY CROPS ; WATER-USE EFFICIENCY ; GENE-EXPRESSION ; LOESS PLATEAU ; REVEALS ; TRANSCRIPTOME ; STRESS ; SEQUENCE ; IDENTIFICATION
语种	英语
出版者	BMC
WOS记录号	WOS:000402400000004
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31500186] ; Key Program of the National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91131902]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/22301]
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Special Agr, Wuhan Bot Garden, Wuhan 430074, Hubei, Peoples R China 3.Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China 6.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Xu, Qin,Song, Zhihong,Zhu, Caiyun,et al. Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change[J]. BMC PLANT BIOLOGY,2017,17.
APA	Xu, Qin.,Song, Zhihong.,Zhu, Caiyun.,Tao, Chengcheng.,Kang, Lifang.,...&Sang, Tao.(2017).Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change.BMC PLANT BIOLOGY,17.
MLA	Xu, Qin,et al."Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change".BMC PLANT BIOLOGY 17(2017).