Integrated transcriptomic and metabolomic analyses delineate the biosynthetic pathways of functional components in maturing Akebia trifoliata fruit

This study integrates transcriptomic and metabolomic analyses across five developmental stages of <i>Akebia trifoliata</i>, a climacteric fruit, to map the molecular mechanisms of fruit maturation. We identified key transcription factors, including NAC, MYB, and AP2/ERF families, and genes orchestrating a stage-specific metabolic transition. Early ripening stages were defined by flavonoid biosynthesis for protection and the initiation of starch degradation, supported by elevated expression of sucrose synthase, amylases, and alpha-amylase. Mid-stages featured enhanced phenolic synthesis, significant protein turnover, alongside differentially expressed cytochrome, E3 ubiquitin ligase, and glucan hydrolases. Final maturation was marked by a dramatic induction of invertase, leading to a surge in sucrose and fructose accumulation responsible for the fruit's characteristic sweetness. This work provides a comprehensive roadmap of ripening, revealing the coordination of flavonoid, hormonal, and carbohydrate pathways. These findings offer promising candidate genes and key metabolic markers associated with fruit quality traits. These findings provide a valuable genomic resource and lay the groundwork for future functional studies aimed at improving the nutritional value and sweetness of <i>A. trifoliata</i> through modern breeding techniques.