Integrated analyses reveal drought responsive microRNAs and their target genes in cucumber

Cucumber (Cucumis sativus), a key vegetable crop, is highly sensitive to water deficiency. MicroRNAs (miRNAs ) are small non-coding RNAs (18–25 nucleotides), which regulate gene expression via sequence-specific binding, and are crucial for plant growth, development, and stress responses. To explore drought-responsive miRNAs and their targets in C. sativus, transcriptome, miRNA, and degradome sequencing were conducted on drought-stressed cucumber leaves. A total of 7,871 differentially expressed mRNAs and 57 differentially expressed miRNAs (55 known and 2 novel) were identified. Degradome analysis revealed 43 miRNAs targeting 129 genes, forming 164 miRNA-target gene pairs, which were primarily involved in secondary metabolite biosynthesis and abiotic stress responses. Among them, 11 key miRNA-target gene pairs linked to drought response were highlighted. This study offered valuable molecular insights into miRNA-mediated drought regulation in cucumbers, thereby contributing our understanding of their stress adaptation mechanisms.