Comparative transcriptomic analysis of two Cucumis melo var. saccharinus germplasms differing in fruit physical and chemical characteristics

BACKGROUND: Hami melon (Cucumis melo var. saccharinus) is a popular fruit in China because of its excellent taste, which is largely determined by its physicochemical characteristics, including flesh texture, sugar content, aroma, and nutrient composition. However, the mechanisms by which these characteristics are regulated have not yet been determined. In this study, we monitored changes in the fruits of two germplasms that differed in physicochemical characteristics throughout the fruit development period. RESULTS: Ripe fruit of the bred variety ‘Guimi’ had significantly higher soluble sugar contents than the fruit of the common variety ‘Yaolong.’ Additionally, differences in fruit shape and color between these two germplasms were observed during development. Comparative transcriptome analysis, conducted to identify regulators and pathways underlying the observed differences at corresponding stages of development, revealed a higher number of differentially expressed genes (DEGs) in Guimi than in Yaolong. Moreover, most DEGs detected during early fruit development in Guimi were associated with cell wall biogenesis. Temporal analysis of the identified DEGs revealed similar trends in the enrichment of downregulated genes in both germplasms, although there were differences in the enrichment trends of upregulated genes. Further analyses revealed trends in differential changes in multiple genes involved in cell wall biogenesis and sugar metabolism during fruit ripening. CONCLUSIONS: We identified several genes associated with the ripening of Hami melons, which will provide novel insights into the molecular mechanisms underlying the development of fruit characteristics in these melons. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03550-8.