Abstract
BackgroundCopper (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.ResultsTolerance 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.ConclusionsA 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.
Highlights
Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms
Base on gene ontology (GO) annotation, we found that most differentially expressed mRNAs (DEmRNAs) in the leaf and root were annotated to the metabolic process, single-organism process, localization process and response to stimulus under biological process (BP), to membrane, cell, organelle, and extracellular region under cellular component (CC), and to binding, catalytic activity, transporter activity, antioxidant activity, transcription factor activity and nutrient reservoir activity under molecular function (MF) (Additional file 10: Figure S1a and b)
The similar changes were found for miR157c-3P and miR535c, as well as their targeted mRNAs and long non-coding RNAs (lncRNAs). These results suggest that the Cu-tolerant XC had occurred much more drastic expression of the Cu-related miRNAs, mRNAs and lncRNAs under Cu toxicity, which may be the important reason that leads to higher Cu tolerance in XC
Summary
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. Copper (Cu) is an essential micronutrient for plant growth and development. Excessive Cu inhibits plant growth and uptake of other mineral nutrients and alters enzyme systems, membrane integrity and many other biochemical and physiological processes [5]. In the last decades, Cu contamination has become a global issue due to the long-term use of Cu-containing fungicides and bactericides, wastewater irrigation, and unconscionable Cu mining [6, 7]. It is important and pressing to gain better understanding of physiological and molecular responses to Cu excess
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