Genome-wide identification and functional analysis of long noncoding RNAs responsive to abscisic acid, drought, and methyl jasmonate in Arabidopsis thaliana.

Long non-coding RNAs (lncRNAs) are pivotal regulators of plant hormone and stress responses, however the lncRNAs that coordinately integrate abscisic acid (ABA), drought, and jasmonate signaling in Arabidopsis thaliana remain poorly understood. A combined bioinformatic and experimental approach was employed to identify stress-responsive lncRNAs and assess their regulatory functions. A total of 447 RNA-seq datasets from ABA, drought, and methyl jasmonate (MeJA) treated samples were analyzed to predict treatment specific lncRNAs, and a core set of multi-stress-responsive lncRNAs (mslncRNAs) was identified by intersecting lncRNA loci across conditions. This analysis identified 4176, 4886, and 4190 lncRNAs under ABA, MeJA, and drought, respectively, 54.33% of which were novel. Differential expression analysis yielded 2318, 2603, and 1788 stress-responsive lncRNAs, and a stringent filtering pipeline defined 287 high-confidence mslncRNAs. Functional enrichment of cis-neighboring genes implicated mslncRNAs in pathogen defense, phytohormone signaling, and abiotic stress responses. Competitive endogenous RNA (ceRNA) network analysis identified 232 endogenous target mimics (eTMs) interacting with 118 miRNAs whose targets are enriched in hormone signaling, stress responses, and core metabolic pathways, indicating that mslncRNAs act as molecular nodes within stress-responsive transcriptional networks. For the experimental validation firstly the expression of the candidate mslncRNA-84 and mslncRNA-189 was validated by RT-qPCR, and their induction by ABA, drought, and MeJA was consistent with in silico predictions. To further characterize their functions, T-DNA insertion lines disrupting these transcripts were subjected to ABA-sensitive germination and jasmonate-dependent growth inhibition assays, biotic stress assays with Pseudomonas syringae pv. tomato DC3000 (including DAB and trypan blue staining and colony-forming unit quantification), and drought survival assays. Collectively, these genome-wide and experimental data indicate that mslncRNAs represent candidate ceRNA-associated regulatory nodes that may contribute to crosstalk among ABA, drought, and MeJA signaling pathways, shaping stress-responsive transcriptional programs.