Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA–miRNA–mRNA regulatory networks in the cotton response to drought stress

竞争性内源性RNA 小RNA 生物 计算生物学 非编码RNA 核糖核酸 干旱胁迫 基因 小RNA 遗传学 长非编码RNA 植物
作者
Baoqi Li,Cheng Feng,Wenhao Zhang,Simin Sun,Dandan Yue,Xianlong Zhang,Xiyan Yang
出处
期刊:International Journal of Biological Macromolecules [Elsevier BV]
卷期号:253: 126558-126558 被引量:12
标识
DOI:10.1016/j.ijbiomac.2023.126558
摘要

Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
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