Preliminary exploration of developmental characteristics of almond flesh based on transcriptome and metabolome combined analysis

Almond, as one of the most important nut tree species worldwide, has been extensively studied for its kernel flavor, lipid composition, and medicinal properties. However, the molecular regulatory mechanisms underlying its flesh development remain largely unexplored. Therefore, this study conducted integrated transcriptomic and metabolomic analyses on flesh samples of the ‘Wanfeng’ almond fruit at five developmental stages. Transcriptome sequencing generated 107.25 Gb of Clean Data, with thousands of differentially expressed genes identified between adjacent stages, indicating dynamic transcriptional reprogramming during flesh development. Enrichment analyses revealed that early and middle developmental stages were primarily associated with cellular development, photosynthesis, and biosynthesis, while later stages were linked to substrate decomposition and programmed cell death. The plant hormone signal transduction pathway played a critical regulatory role in almond flesh development. Metabolomic profiling identified 6,528 metabolites, with most differential metabolites accumulating before DAF96. Metabolite classification highlighted six dominant categories, including Fatty Acyls and Organooxygen compounds. Integrated analysis demonstrated the involvement of the phenylpropanoid biosynthesis pathway in lignin synthesis, which likely regulates cellular structure, stability, and flesh hardness throughout development. The hierarchical network model provides novel insights into the temporal regulation of almond flesh development, particularly the regulatory axis centered on 4CL and its interacting transcription factors, laying a theoretical foundation for subsequent functional validation. The qRT-PCR results highlight dynamic transcriptional regulation of key genes across six phytohormone and phenylpropanoid biosynthesis pathways during flesh development in almond. This study provides data reference for subsequent exploration of the regulation mechanism of almond flesh development.