Establishment of comparative transcriptome dataset related to nitrogen use efficiency in melon

Nitrogen use efficiency (NUE) is a key physiological trait influencing yield formation and resource utilization in melon (Cucumis melo var. saccharinus). To elucidate the molecular mechanisms underlying differential NUE among melon cultivars, we performed transcriptome profiling of four inbred lines with contrasting NUE-T514 and T55 (N-efficient) and T213 and T23 (N-inefficient)-grown under high-nitrogen (HN) and low-nitrogen (LN) conditions. A total of 24 leaf samples collected during the fruit-expansion stage were subjected to Illumina RNA-seq, generating 160.31 Gb of high-quality clean reads with > 94% mapping efficiency. We annotated 26,222 expressed genes, including 644 newly predicted genes, and constructed the longest transcript dataset. Pearson correlation analysis and PCA confirmed excellent sample reproducibility and clear transcriptomic separation among germplasms and N treatments. Differential expression analysis revealed 824 core DEGs consistently associated with NUE across eight pairwise comparisons. Six representative DEGs were validated by RT-qPCR, showing strong concordance with RNA-seq results. These results provide valuable molecular resources for improving NUE in melon, with potential applications in reducing fertilizer input and increasing productivity.