Construction of a ceRNA regulatory network in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) based on whole-genome transcriptome profiling of mRNAs, lncRNAs, miRNAs and circRNAs under Cu toxicity

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 molecular response of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) to Cu toxicity and to construct their competing endogenous RNAs (ceRNAs) network in citrus.Results In this study, tolerance of four commonly used rootstocks to Cu toxicity was first evaluated, and ‘Ziyang Xiangcheng’ (Citrus junos ) was proved to be tolerant rootstock. Then the Cu-treated and -untreated root (CuR, CKR) and leaf (CuL, CKL) of ‘Ziyang Xiangcheng’ was selected to perform whole-genome 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 CuR/CKR and CuL/CKL, respectively. Gene ontology enrichment analysis of these DEmRNAs and targets of DElncRNAs and DEmiRNAs showed that most were annotated to oxidation-reduction, phosphorylation, membrane, and ion binding. The ceRNA network was constructed with the predicted DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs pairs, which further revealed regulatory roles of these DERNAs in Cu toxicity.Conclusions A large number of mRNAs, lncRNAs, circRNAs, and miRNAs were altered in response to Cu toxicity in citrus, and they may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network.