A systematic identification and characterization of long noncoding RNAs during abiotic stress in Medicago truncatula

Abiotic stresses significantly affect plant growth and development, and long non-coding RNAs (lncRNAs) have emerged as key regulators of plant stress responses. However, a systematic characterization of lncRNAs landscapes across multiple abiotic stresses in Medicago truncatula remains lacking. In particular, the coordinated roles of lncRNAs under diverse stress conditions and their potential regulatory relationships remain poorly understood. In this study, we analyzed 54 public RNA-seq datasets of Medicago truncatula under seven stress conditions and identified 6,449 lncRNAs, including 4,115 novel and 2,334 known lncRNAs. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis revealed stress-responsive lncRNAs, including co-expressed lncRNAs in key modules and differentially expressed lncRNAs under cold, drought and salt stress. Functional enrichment analysis indicated that these were involved in intracellular components, cellular component biogenesis, and metabolic processes. Furthermore, we predicted that seven lncRNAs may serve as potential precursors of 20 miRNAs. Under cold stress, eight putative lncRNAs MtCIRs were predicted based on their expression levels and chromosomal locations relative to MtCBFs genes, among which MtCIR1 and MtCIR3-1 exhibited the highest sequence similarity. In summary, this study provides a comprehensive landscape of stress-responsive lncRNAs in M. truncatula and offers testable hypotheses as well as valuable resources for the future functional characterization of lncRNAs in legume stress adaptation.