IB-CAS  > 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
2020
Source PublicationBMC PLANT BIOLOGY
ISSN1471-2229
Volume20Issue:1
AbstractBackground 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.
KeywordCBFs Cold stress Long non-coding RNAs Medicago truncatula MtCIR1
Subject AreaPlant Sciences
DOI10.1186/s12870-020-2301-1
Indexed BySCI
Language英语
WOS KeywordLONG NONCODING RNAS ; GENOME-WIDE IDENTIFICATION ; FREEZING TOLERANCE ; FUNCTIONAL PREDICTION ; TRANSCRIPTION FACTORS ; STRESS TOLERANCE ; GENE-EXPRESSION ; SALT STRESS ; ACCLIMATION ; ARABIDOPSIS
WOS Research AreaPlant Sciences
WOS IDWOS:000519055700001
PublisherBMC
SubtypeArticle
Publication PlaceLONDON
Funding OrganizationNational Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31671270] ; Chinese Academy of SciencesChinese Academy of Sciences [KFJ-STS-ZDTP-056]
Corresponding Author Emailwhzhang@ibcas.ac.cn
OAgold, Green Published
Citation statistics
Cited Times:10[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/21865
Collection植被与环境变化国家重点实验室
Affiliation1.[Zhao, Mingui
2.Wang, Tianzuo
3.Sun, Tianyang
4.Yu, Xiaoxi
5.Tian, Rui
6.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China
7.Chinese Acad Sci, Beijing Inst Life Sci, Res Network Global Change Biol, Beijing 100101, Peoples R China
8.[Sun, Tianyang
9.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
10.Chinese Acad Sci, Inner Mongolia Res Ctr Prataculture, Beijing 100093, Peoples R China
Recommended Citation
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).
Files in This Item:
File Name/Size DocType Version Access License
Zhao-2020-Identifica(2462KB)期刊论文出版稿开放获取CC BY-NC-SAView Application Full Text
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Zhao, Mingui]'s Articles
[Wang, Tianzuo]'s Articles
[Sun, Tianyang]'s Articles
Baidu academic
Similar articles in Baidu academic
[Zhao, Mingui]'s Articles
[Wang, Tianzuo]'s Articles
[Sun, Tianyang]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Zhao, Mingui]'s Articles
[Wang, Tianzuo]'s Articles
[Sun, Tianyang]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: Zhao-2020-Identification of tissue-specific an.pdf
Format: Adobe PDF
This file does not support browsing at this time
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.