**1. Introduction**

Since the proposal of the central dogma of molecular biology in 1961, RNA has been considered an intermediate that translates genetic information from DNA to protein [1,2]. However, with the discovery of noncoding RNAs (ncRNAs), we found that intermediate RNAs represent a fraction of all RNAs [2,3]. As the main products of the eukaryotic transcriptome, ncRNAs function as structural, catalytic, or regulatory RNAs rather than as protein encoders [2,4–6]. Based on RNA length, regulatory ncRNAs can be further classified as small ncRNAs (<200 bp, e.g., miRNAs, siRNAs, and piRNAs) or long ncRNAs (lncRNAs) (>200 bp, e.g., lincRNAs and macroRNAs) [2,7]. In the early 1990s, with the appearance of the X-chromosome-silencing phenomenon, long ncRNAs (lncRNAs) were first discovered, having once been considered the 'dark matter' of transcriptomes [8]. Recently, lncRNAs have been discovered to have strong and universal regulatory effects on gene expression at the post-transcriptional, transcriptional, and epigenetic levels [9–13].

lncRNAs play important roles in many biological processes in plants, especially in developmental regulation and stress responses [14–16]. A total of 1832 lncRNAs in Arabidopsis were changed after cold, drought, high-salt, and abscisic acid (ABA) treatments [17]. Several lncRNAs, such as COLDAIR and COOLAIR, positively respond to cold and function in flowering induction [18,19]. IPS1 and At4, induced by phosphate starvation, regulate

**Citation:** Liang, G.; Niu, Y.; Guo, J. Systematic Identification of Long Non-Coding RNAs under Allelopathic Interference of Para-Hydroxybenzoic Acid in *S. lycopersicum*. *Horticulturae* **2022**, *8*, 1134. https://doi.org/10.3390/ horticulturae8121134

Academic Editor: Sergey V. Dolgov

Received: 30 September 2022 Accepted: 22 November 2022 Published: 2 December 2022

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**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

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the shoot dynamic balance of phosphate through the blockage of the repression of miR399 on its target gene, PHO2 [20–23]. Further exploration of the function of lncRNAs in plant responses to stress would provide approaches to discover the stress response networks [24].

As an important factor affecting agricultural production, allelopathy has become a hot topic in ecology, horticulture, agronomy, and other research areas [25–29]. Allelochemicals have been proven to be responsible for numerous biochemical and physiological changes that cause plant allelopathy [30,31]. The plant growth regulatory system, respiration, photosynthesis, the antioxidant system, and water and nutrient uptake are the key physiological and biochemical systems and processes in plants in which changes are induced by allelochemicals [32,33].

Transcription factors, DNA methylation events, chromatin modifications, and microRNAs have been discovered in the gene regulatory processes described above [34–37]. LncRNAs are critical in plant gene expression regulation in response to stress [38–40], which indicates that lncRNAs might also function in plant response to allelopathy. The involvement of lncRNAs in gene transcription regulation progress have not been explored. The expression of most lncRNAs is tissue-specific, which allows them to be discovered by transcriptome sequencing (RNA-seq). By examining RNA-seq data of leaves under salt stress, long noncoding RNAs were identified and characterized in *Medicago truncatula* [41].

However, plant allelopathy is a complex process. To explore the allelopathy network in plants, it is necessary to study the dynamic changes in gene expression under different degrees of stress. The roles of lncRNAs in plant allelopathy in *S. lycopersicum* were explored in this study. Firstly, lncRNAs expressed in *S. lycopersicum* leaves under different PHBA treatments were identified with RNA-seq. Next, cis- and trans-regulated target PGs (TTPGs) for lncRNAs were predicted, and the coexpressions between lncRNAs and their targets were analyzed. Third, the conservation of lncRNAs in *S. lycopersicum* and *Ahrabidopsis thaliana* was compared. Lastly, we explored the possibility that these lncRNAs might be endogenous pseudotarget mimics (eTMs) of known *S. lycopersicum* miRNAs. Overall, this study helps to understand the role of lncRNAs in the molecular network of plant allelopathy and gives new clues about plant response to stress.

#### **2. Materials and Methods**
