Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

Abstract

Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

“…This type of lncRNA is termed an endogenous target mimic (eTM) (Wu et al, 2013). Jiang et al (2019) reported that the tomato lncRNA23468 functions as an eTM to modulate NBS-LRR genes by mimicking miR482b in the tomato-P. infestans interaction. In this study, 12 lncRNAs were predicted to be target mimics of 17 known mature miRNAs.…”

Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering

“…Similarly, several lncRNAs function by interacting with miRNAs in other plant species (Hao et al, 2015;Wang et al, 2015;Deng et al, 2018;Chen et al, 2018a). Furthermore, nta-eTMX27 in Nicotiana tabacum , osa-eTM160 in Oryza sativa (Wang et al, 2017a), lncRNA23468 in Solanum lycopersicum (Jiang et al, 2019), and LTCONS-00042843 in Dimocarpus longan (Chen et al, 2018a) are eTMs that modulate target gene expression by functioning as decoys for relevant miRNAs. The development of high-throughput sequencing and bioinformatics tools enabled the identification of many lncRNAs in several plant species, including model plants like A. thaliana (Yuan et al, 2016), O. sativa (Zhang et al, 2014;Wang et al, 2018a), and Brachypodium distachyon (Quattro et al, 2017), and also in horticultural plants such as S. lycopersicum (Zhu et al, 2015), Cucumis sativus (Hao et al, 2015), Musa itinerans (Liu et al, 2018a), D. longan (Chen et al, 2018a), and Citrus sinensis (Ke et al, 2019).…”

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

“…In A. thaliana, lncRNAs reportedly enhance the resistance to Pseudomonas syringae pv. tomato DC3000 by promoting PR1 expression [40]. In tomato, lncRNA23468 functions as a ceRNA that modulates NBS-LRR gene expression by mimicking the target of miR482b, thereby increasing the resistance to P. infestans [41].Walnut anthracnose has been responsible for the premature fruit drop and yield losses that have adversely affected walnut production in China [7].…”