Identification and Analysis Long Noncoding RNA in Response to Cold Stress in Cucumber

Long noncoding RNAs (lncRNAs) are crucial components of plant genomes, often exceeding the number of protein-coding genes. Although recent studies have highlighted the importance of plant lncRNAs in low-temperature responses, the identification and characterization of lncRNAs in cucumber ( Cucumis sativus L.) under cold stress remain unexplored. In this study, we analyzed 33,325 assembled transcripts derived from RNA-Seq data of six cucumbers exposed to normal and low-temperature conditions. From these, we identified and annotated 256 lncRNAs. Comparative analysis revealed that these lncRNAs generally contained fewer exons but exhibited longer transcript lengths than cucumber protein-coding genes. Among the annotated lncRNAs, 118 (46.10%) were located in intergenic regions, and 88 (52 upregulated and 36 downregulated) showed differential expression under cold stress. Further investigation identified six protein-coding genes and five lncRNAs associated with turquoise co-expression module linked to chilling tolerance in cucumber. The stress-responsive roles of these five lncRNAs were validated through quantitative polymerase chain reaction experiments. This study provides a comprehensive annotation of cucumber lncRNAs using RNA-Seq data and offers insights into their potential regulatory functions in cold stress responses. Our findings serve as a valuable resource for future research on the molecular mechanisms underlying low-temperature adaptation in cucumber.