Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

doi:10.1186/s12870-020-2301-1

CORC > 植物研究所 > 中国科学院植物研究所 > 植被与环境变化国家重点实验室

	Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing
	Zhao, Mingui ; Wang, Tianzuo ; Sun, Tianyang ; Yu, Xiaoxi ; Tian, Rui ; Zhang, Wen-Hao
刊名	BMC PLANT BIOLOGY
	2020
卷号	20 期号:1
关键词	CBFs Cold stress Long non-coding RNAs Medicago truncatula MtCIR1
ISSN号	1471-2229
DOI	10.1186/s12870-020-2301-1
文献子类	Article
英文摘要	Background Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. Results RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distributed across the eight chromosomes in M. truncatula seedlings with obvious preferences for locations. Further analyses revealed that the cold-responsive lncRNAs differed between leaves and roots. The putative target genes of the lncRNAs were predicted to mainly involve the processes of protein translation, transport, metabolism and nucleic acid transcription. Furthermore, the networks of a tandem array of CBF/DREB1 genes that were reported to be located in a major freezing tolerance QTL region on chromosome 6 and their related lncRNAs were dissected based on their gene expression and chromosome location. Conclusions We identified a comprehensive set of lncRNAs that were responsive to cold treatment in M. truncatula seedlings, and discovered tissue-specific cold-responsive lncRNAs in leaves and roots. We further dissected potential regulatory networks of CBF Intergenic RNA (MtCIR1) and MtCBFs that play critical roles in response and adaptation of M. truncatula to cold stress.
学科主题	Plant Sciences
出版地	LONDON
WOS关键词	LONG NONCODING RNAS ; GENOME-WIDE IDENTIFICATION ; FREEZING TOLERANCE ; FUNCTIONAL PREDICTION ; TRANSCRIPTION FACTORS ; STRESS TOLERANCE ; GENE-EXPRESSION ; SALT STRESS ; ACCLIMATION ; ARABIDOPSIS
WOS研究方向	Plant Sciences
语种	英语
出版者	BMC
WOS记录号	WOS:000519055700001
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31671270] ; Chinese Academy of SciencesChinese Academy of Sciences [KFJ-STS-ZDTP-056]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21865]
专题	植被与环境变化国家重点实验室
作者单位	1.Sun, Tianyang 2.[Zhao, Mingui 3.Wang, Tianzuo 4.Chinese Acad Sci, Beijing Inst Life Sci, Res Network Global Change Biol, Beijing 100101, Peoples R China 5.[Sun, Tianyang 6.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 7.Chinese Acad Sci, Inner Mongolia Res Ctr Prataculture, Beijing 100093, Peoples R China 8.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China 9.Tian, Rui 10.Yu, Xiaoxi
推荐引用方式 GB/T 7714	Zhao, Mingui,Wang, Tianzuo,Sun, Tianyang,et al. Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing[J]. BMC PLANT BIOLOGY,2020,20(1).
APA	Zhao, Mingui,Wang, Tianzuo,Sun, Tianyang,Yu, Xiaoxi,Tian, Rui,&Zhang, Wen-Hao.(2020).Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing.BMC PLANT BIOLOGY,20(1).
MLA	Zhao, Mingui,et al."Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing".BMC PLANT BIOLOGY 20.1(2020).