全转录组 RNA 测序揭示了紫阳香橙（Citrus junos Sieb. Ex Tanaka）响应铜毒性的全局分子反应以及 mRNA、lncRNA、miRNA 和 circRNA 的 ceRNA 调控网络。

Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka).

机构信息

Citrus Research Institute, Southwest University, Chongqing, 400712, China.

Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China.

出版信息

BMC Plant Biol. 2019 Nov 21;19(1):509. doi: 10.1186/s12870-019-2087-1.

BACKGROUND

Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms. This study aims to uncover the global landscape of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in response to Cu toxicity so as to construct a regulatory network of competing endogenous RNAs (ceRNAs) and to provide valuable knowledge pertinent to Cu response in citrus.

RESULTS

Tolerance of four commonly used rootstocks to Cu toxicity was evaluated, and 'Ziyang Xiangcheng' (Citrus junos) was found to be the most tolerant genotype. Then the roots and leaves sampled from 'Ziyang Xiangcheng' with or without Cu treatment were used for whole-transcriptome sequencing. In total, 5734 and 222 mRNAs, 164 and 5 lncRNAs, 45 and 17 circRNAs, and 147 and 130 miRNAs were identified to be differentially expressed (DE) in Cu-treated roots and leaves, respectively, in comparison with the control. Gene ontology enrichment analysis showed that most of the DEmRNAs and targets of DElncRNAs and DEmiRNAs were annotated to the categories of 'oxidation-reduction', 'phosphorylation', 'membrane', and 'ion binding'. The ceRNA network was then constructed with the predicted pairs of DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs, which further revealed regulatory roles of these DERNAs in Cu toxicity.

CONCLUSIONS

A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in 'Ziyang Xiangcheng' were altered in response to Cu toxicity, which may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network in this Cu-tolerant rootstock.

背景

铜（Cu）毒性已成为柑橘生产的潜在威胁，但相关机制知之甚少。本研究旨在揭示 Cu 毒性响应中的 mRNA、长非编码 RNA（lncRNA）、环状 RNA（circRNA）和 microRNA（miRNA）的全局图谱，构建竞争内源性 RNA（ceRNA）的调控网络，并为柑橘中 Cu 响应提供有价值的知识。

结果

评估了四种常用砧木对 Cu 毒性的耐受性，发现‘紫阳香橙’（Citrus junos）是最耐受的基因型。然后，用 Cu 处理或未处理的‘紫阳香橙’的根和叶进行了全转录组测序。与对照相比，Cu 处理的根和叶中分别有 5734 个和 222 个 mRNAs、164 个和 5 个 lncRNA、45 个和 17 个 circRNA、147 个和 130 个 miRNA 差异表达（DE）。基因本体富集分析表明，大多数 DEmRNA 和 DElncRNA 和 DEmiRNA 的靶基因被注释为“氧化还原”、“磷酸化”、“膜”和“离子结合”类别。然后，用预测的 DEmRNAs-DEmiRNAs 和 DElncRNAs-DEmiRNAs 对 ceRNA 网络进行了构建，进一步揭示了这些 DERNAs 在 Cu 毒性中的调控作用。