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Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava

文献类型： 外文期刊

作者： Ding, Zehong 1 ; Tie, Weiwei 1 ; Fu, Lili 1 ; Yan, Yan 1 ; Liu, Guanghua 2 ; Yan, Wei 2 ; Li, Yanan 2 ; Wu, Chunlai 1 ; Zhan 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Key Lab Biol & Genet Resources Trop Crops, Inst Trop Biosci & Biotechnol, Xueyuan Rd 4, Haikou, Hainan, Peoples R China

2.Yunnan Acad Agr Sci, Inst Trop & Subtrop Cash Crops, Baoshan, Yunnan, Peoples R China

3.Huazhong Univ Sci & Technol, Chinese Natl Ctr Plant Gene Res Wuhan HUST Part, Key Lab Mol Biophys,Coll Life Sci & Technol,Chine, Genet Engn Int Cooperat Base,Chinese Minist Sci &, Wuhan, Hubei, Peoples R China

关键词： Cassava; lncRNA; PEG treatment; Tissue-specific expression; ssRNA-Seq

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷

页码：

收录情况： SCI

摘要： BackgroundLong noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance.ResultsIn this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR.ConclusionsThese findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future.

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