*Article* **Systematic Identification of Long Non-Coding RNAs under Allelopathic Interference of Para-Hydroxybenzoic Acid in** *S. lycopersicum*

**Guoting Liang 1, Yajie Niu <sup>2</sup> and Jing Guo 2,\***


**Abstract:** The importance of long noncoding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of the lncRNAs expressed during plant allelopathy has not been carried out. We performed RNA-seq experiments on *S. lycopersicum* subjected to different levels of para-hydroxybenzoic acid (PHBA) stress during plant allelopathy and identified 61,729 putative lncRNAs. Of these, 7765 lncRNAs cis-regulated 5314 protein-coding genes (PGs). Among these genes, 1116 lncRNAs and 2239 PGs were involved in a complex web of transcriptome regulation, and we divided these genes into 12 modules. Within these modules, 458 lncRNAs and 975 target genes were found to be highly correlated. Additionally, 989 lncRNAs trans-regulated 1765 PGs, and we classified them into 11 modules, within which 335 lncRNAs were highly correlated with their 633 corresponding target genes. Only 98 lncRNAs in *S. lycopersicum* had homologs in the lncRNA database of *Arabidopsis thaliana*, all of which were affected by the PHBA treatments. MiRNAs that interacted with both mRNAs and lncRNAs were selected on the basis of weighted correlation network analysis (WGCNA) results to make lncRNA-miRNA-mRNA triplets. Our study presents a systematic identification of lncRNAs involved in plant allelopathy in *S. lycopersicum* and provides research references for future studies.

**Keywords:** *S. lycopersicum*; long noncoding RNAs; allelopathy; cis-regulatory; trans-regulatory; endogenous target mimics; transcriptome
