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

文献类型：期刊论文

作者Zhao, Mingui; Wang, Tianzuo; Sun, Tianyang; Yu, Xiaoxi; Tian, Rui; Zhang, Wen-Hao
刊名BMC PLANT BIOLOGY
出版日期2020
卷号20期号:1
ISSN号1471-2229
关键词CBFs Cold stress Long non-coding RNAs Medicago truncatula MtCIR1
DOI10.1186/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]
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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Wang, Tianzuo
5.Sun, Tianyang
6.Yu, Xiaoxi
7.Tian, Rui
8.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China
9.Chinese Acad Sci, Inner Mongolia Res Ctr Prataculture, Beijing 100093, Peoples R China
10.Chinese Acad Sci, Beijing Inst Life Sci, Res Network Global Change Biol, Beijing 100101, Peoples R China
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).

入库方式： OAI收割

来源：植物研究所

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