Differential and Specific Analysis of Free Amino Acid Composition in Cucurbitaceae Fruits: A Multi-Tissue Study of 10 Species

Free amino acids serve as a crucial hub connecting plant life activities with human nutrition. The fruits of Cucurbitaceae crops are natural nitrogen reservoirs, rich in free amino acids such as citrulline, arginine, and γ-aminobutyric acid (GABA). To investigate the spatial accumulation characteristics and differential distribution of free amino acids in cucurbit fruits, this study measured the contents of 19 free amino acids in the fruit stem, epicarp, endocarp, pulp, and seeds of 10 cucurbit species (12 varieties) at the mature stage. The results revealed that free amino acid accumulation exhibits significant tissue specificity and species specificity, forming diverse nitrogen metabolism hubs. Glutamine, aspartate, asparagine, arginine, and citrulline constitute a highly coordinated core module of nitrogen metabolism in Cucurbitaceae. Methionine, valine, and some other amino acids were consistently present at extremely low levels across tissues, indicating a competitive diversion of conserved metabolic pathways coexisting among species. Species classification based on free amino acids differed markedly from traditional taxonomy based on gene domestication, implying environmental selection pressures and non-linear gene-metabolite network relationships. Glutamine, GABA, citrulline, and arginine were identified as core hub metabolites supporting tissue type classification. This study revealed the allocation characteristics of free amino acids in fruits of various cucurbit crops and established a functional model integrating nitrogen assimilation, flavor/energy metabolism, stress tolerance/defense signaling, and storage across different tissue types of multiple cucurbit crops, providing new perspectives for precision breeding and domestication mechanism research in Cucurbitaceae.