Transcriptome and metabolome analysis of fruit firmness and organic acids in two different varieties of melon ( Cucumis melo L.)

Fruit firmness and organic acids are important indicators to evaluate the commerciality of melon. However, the transformation processes of firmness and metabolomics in different melon fruits remain unclear. In this study, two melon varieties (named processing-type Baogua and edible-type M15) were used to analyze the firmness and organic acids at the growth stage of 28 days. The transcriptome and metabolome of fruits were explored to clarify gene expression and metabolites. A total of 4370 genes were up-regulated and 2447 genes were down-regulated in Baogua when compared to M15. The Gene Ontology analysis of differentially expressed genes in cell components was the highest for the cell periphery, followed by the membrane, extracellular region, and external encapsulating structures. Furthermore, a total of 54 differential metabolites were identified in the two melon fruits. Citric acid, tryptophan, and proline were accumulated in M15 fruits. Amino acids, such as threonine, norleucine, histidine, and glutamic acid, were reduced in Baogua fruits. RT-qPCR analysis showed that polygalacturonase and aconitate hydratase genes were related to the fruit firmness and citric acid contents. The up-regulation of ACO genes could increase citric acid content in M15 when compared to Baogua. The findings provide a new understanding of the citric acid transformation and help to control the quality of melon fruits during the storage or shelf-lifetime.