Key metabolic pathways across sponge gourd (Luffa aegyptiaca Mill.) development and ripening

Sponge gourd ( Luffa aegyptiaca Mill.), is renowned for its high nutritional value and diverse medicinal properties. Few studies have explored the interaction between dynamic gene expression patterns and nutrient regulatory networks of sponge gourd. Utilizing transcriptomics and metabolomics in conjunction with weighted gene co-expression network analysis (WGCNA), we analyzed gene and metabolite changes throughout the entire developmental cycle of the sponge gourd, from 1 day-post-anthesis (DPA) to 50 DPA. We constructed a regulatory model of the interactions between target genes and their essential metabolites in key metabolic pathways—including flavonoids, phenolic acids, pectin polysaccharides, and amino acids—during maturation and senescence. We found that transcription factor MYB25, flavonol synthase ( FLS ), shikimate o-hydroxycinnamoyltransferase ( HCT ), caffeoylshikimate esterase ( CSE ), and other important genes in the flavonoid and phenolic acid pathways, played a key role in regulating the maturation and senescence of the sponge gourd fruit. In addition, we observed dynamic regulation of pectin polysaccharides and various amino acid derivatives, such as PG , PAE10 , PL12 , GAD , AST , GLUD2 and transcription factor ERF12, bZIP5. Our results provide new insights into the metabolic regulatory network and its changes throughout the development and ripening of the sponge gourd and serve as a valuable reference for metabolic studies of other Cucurbit species.