Widely Untargeted Metabolomics Profiling Combined with Transcriptome Analysis Provides New Insight into Amino Acid Biosynthesis at Different Developmental Stages of <i>Rubus Chingii</i> Hu (Chinese Raspberry)

The composition and profile of amino acids in <i>Rubus chingii (R. chingii)</i> Hu serve as critical indicators of its nutritional quality. A comprehensive understanding of the amino acid metabolism within <i>R. chingii</i> is instrumental in the formulation and innovation of functional foods derived from this species. Utilizing advanced techniques such as wide-ranging untargeted metabolomics, transcriptome analysis, interaction network mapping, heat map analysis, and quantitative real-time PCR, we conducted a comprehensive assessment of the quality attributes across four distinct developmental stages of <i>R. chingii.</i> Our meticulous analysis uncovered a rich tapestry of 76 distinct amino acids and their derivatives within the developmental stages of <i>R. chingii</i>. The spectrum of essential amino acids was not only broad but also displayed a high degree of variety. Notably, leucine, lysine, and phenylalanine stood out as the most abundant amino acids, underscoring their significant presence throughout the growth cycle of <i>R. chingii.</i> The proportion of essential amino acids relative to the total amino acid content in <i>R. chingii</i> exhibited a notable trajectory of change throughout its developmental stages. It began with 30.92% in the immature green phase, advanced to 31.04% during the transition from green to yellow, peaked at 33.62% in the yellow to red stage, and then moderated to 30.43% in the full red phase. This pattern suggests a strategic modulation of amino acid composition, aligning with the evolving nutritional requirements and metabolic shifts as the fruit matures. Concurrent analysis of interaction networks and heat maps, alongside comprehensive profiling of amino acid metabolism and transcriptomic examination, was conducted to elucidate the intricate dynamics of cellular processes. The results showed that seven differentially expressed genes (DEGs) played important roles in amino acid metabolism, including PFK, BCAT1, TSB, ASA, ACO, TOM2AH3, and BCAT2. The expression patterns of seven DEGs conformed closely to the findings revealed by the preceding RNA-seq analysis. In this investigation, we elucidated the regulatory mechanisms underlying amino acid metabolism across the four distinct developmental stages of <i>R. chingii</i> through comprehensive amino acid profiling and transcriptomic analysis. These insights lay the groundwork for the development of novel functional food applications utilizing <i>R. chingii</i>.