Integrated Metabolomics and Transcriptomics Analysis Reveals the Biosynthetic Mechanism of Isoquinoline Alkaloids in Different Tissues of Hypecoum erectum L.

<i>Hypecoum erectum</i> L. is a medicinal plant known for its high content of isoquinoline alkaloids (IQAs), a class of compounds with diverse pharmacological activities. To elucidate the biosynthetic mechanisms and tissue-specific accumulation of IQAs, we integrated HPLC-MS/MS-based metabolomic analysis with RNA sequencing (RNA-seq) transcriptomic profiling across the roots, stems, and leaves of <i>H. erectum.</i> Metabolomic analysis identified twenty-six IQAs as differentially accumulated metabolites (DAMs) among the three tissues, while transcriptomic analysis revealed twenty-two categories of differentially expressed genes (DEGs) involved in IQA biosynthesis. KEGG pathway enrichment analysis demonstrated that nine DAMs and twenty categories of DEGs were co-enriched in the IQA biosynthetic pathway of <i>Hypecoum erectum</i>. Notably, seven key DAMs-Stylopine, Protopine, Magnoflorine, Corydaline, Tetrahydropalmatine, Sanguinarine, and Palmatine-preferentially accumulated in the root, concomitant with the elevated expression of eleven root-specific DEGs, including <i>GOT1</i>, <i>CYP719A14</i>, <i>SMT</i>, <i>CYP719A1</i>_<i>2</i>_<i>3</i>_<i>13</i>, <i>PSOMT1</i>, <i>E2.1.1.116</i>, <i>CYP80B1</i>, <i>E2.1.1.128</i>, <i>NCS</i>, <i>ASP5</i>, and <i>BBE1</i>. Gene-metabolite correlation network analysis further identified nine DAMs and fifteen DEGs closely associated with IQA biosynthesis, highlighting key enzymatic regulators of alkaloid accumulation. Additionally, several transcription factor (TF) families, including bHLH, NAC, and ERF families, were predicted to participate in the transcriptional regulation of IQA-related genes. Collectively, these findings demonstrate that roots are the primary site of IQA biosynthesis in <i>H. erectum</i> and provide a molecular framework for understanding the regulation and utilization of its medicinally active components.