Profiling the accumulation of ten bioactive compounds in <i>Rheum officinale</i> across different growth years using integrated HPLC and transcriptomic approaches

<italic>Rheum officinale</italic> is a prominent traditional medicinal herb in the Chinese Pharmacopeia. Variations in the composition and accumulation of secondary metabolites in <italic>R. officinale</italic> have been observed to correlate with harvest periods. This study investigated the progressive accumulation of six bioactive compounds in the roots and rhizomes of <italic>R. officinale</italic> over three growth years. Comparative transcriptome analyses were performed across three developmental stages of both root and rhizome tissues. In the root tissues, 23 differentially expressed genes (DEGs) were observed, including <italic>CYP450, WRKY, UGT73C5, WAT1</italic>, and <italic>XTH15</italic>, which displayed significant differential expression patterns. Similarly, 14 DEGs in the rhizome tissues showed significant differential expression, encompassing <italic>CYP450</italic>, <italic>WRKY</italic>, and <italic>UGT71A15</italic>. Short Time-series Expression Miner (STEM) analysis revealed that cluster 10 (1,826 genes) in the root tissues was notably enriched in metabolic processes, predominantly involving <italic>WRKY</italic>, <italic>CYP450</italic>, and <italic>HSP</italic> gene families. In rhizome tissues, cluster 9 (3,301 genes) included numerous gene families, with <italic>WRKY,</italic> <italic>CYP450,</italic> and <italic>UGT</italic> as the top three. Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct networks for 3,734 and 1,578 DEGs in root and rhizome tissues, respectively. Hub genes such as <italic>WRKY32</italic> and <italic>CYP82G1</italic> exhibited robust connectivity with other genes, suggesting their pivotal roles in pharmacopoeia indicator biosynthesis in root tissues. Moreover, <italic>CYP76T24, UGT71A15,</italic> and <italic>WRKY44</italic> were identified as crucial genes in pharmacopoeia indicator biosynthesis in rhizome tissues. Collectively, these comprehensive results underscore the involvement of <italic>CYP450</italic> and <italic>UGT</italic> in the biosynthetic pathways of bioactive compounds in <italic>R. officinale.</italic>