Long Noncoding RNA: An Uncharted Territory in Plant Diseases and Immunity

Long noncoding RNAs (lncRNAs) are a class of transcripts longer than 200 nucleotides with little or no protein-coding capacity. They represent a substantial fraction of eukaryotic genomes and function as molecular architects that coordinate diverse biological processes and physiological plasticity, including multilayered plant defence systems, through versatile regulatory interactions at multiple levels of gene regulation. Recent advances in high-throughput RNA sequencing technologies have greatly expanded the identification of plant lncRNAs, revealing their diverse roles as scaffolds, decoys, guides, and regulatory molecules. These lncRNAs are increasingly recognised as integral components of plant immune systems, contributing critically to host defence mechanisms. This review highlights recent progress in lncRNA identification using computational pipelines as well as emerging artificial intelligence (AI) and machine learning (ML) based approaches. We further explore current insights into the regulatory functions of lncRNAs during host-pathogen interactions. Notably, we discuss a paradigm-shifting discovery in lncRNA biology, the finding that many lncRNAs, once presumed to be non-coding, contain small open reading frames (sORFs) that encode functional micropeptides. Modern predictive modelling has been crucial to identify these sORFs and their peptide products and to show that lncRNAs have multiple functions as regulatory transcripts and peptide precursors in plant immunity.