Comparative Metabolomics and Transcriptomics Analysis of Rosa roxburghii Tratt and Rosa kweichonensis var. sterilis

<i>Rosa roxburghii</i> Tratt (RR) and <i>Rosa kweichonensis</i> var. <i>sterilis</i> (RS) are both edible medicinal plants. However, they are often confused due to their similar phenotypic characteristics, which may limit their targeted development and utilization. Here, we integrated targeted metabolomics (UPLC-MS/MS) and transcriptomics (Illumina HiSeq) to systematically dissect the metabolic and transcriptional differences between the two species. Metabolomic profiling identified 558 differentially accumulated metabolites (DAMs), defined as metabolites with significantly different abundance between RS and RR, predominantly classified as flavonoids and phenolic acids. Among these, vitamin C (L-ascorbic acid) and argininosuccinic acid were prioritized as key DAMs based on their significant fold changes, high abundance, and functional relevance to bioactivity and stress tolerance. Transcriptomic analysis further revealed that vitamin C synthesis is primarily driven by the coordinated up-regulation of <i>USP</i> and <i>GME</i> genes in the L-ascorbic acid metabolic pathway, while argininosuccinic acid production, as an intermediate in the urea cycle, is mainly mediated by the up-regulated <i>glnA</i> gene. These findings not only clarify the molecular basis of metabolic divergence between RR and RS but also provide potential biomarkers for their identification, laying a solid foundation for their development as distinct functional foods.