The chromosome-level genome assembly and multi-omics analyses unveil a pivotal regulatory mechanism of Piperlongumine biosynthesis in the Piper sarmentosum

Piper sarmentosum Roxb is a significant medicinal and edible plant, and its active compound piperlongumine (PL) has garnered attention due to its pharmacological activities, including anticancer and anti-inflammatory effects. However, the key enzymes and regulatory mechanisms of its biosynthetic pathway are not fully understood. In this study, we completed a chromosome-level genome assembly of P. sarmentosum by integrating PacBio HiFi, Hi-C, and multi-omics data. The genome size is 548.45 Mb, with a contig N50 of 15.36 Mb and a scaffold N50 of 22.52 Mb. The BUSCO assessment indicated high completeness at 97.4%. Genome annotation revealed 39,154 protein-coding genes and identified two lineage-specific whole-genome duplication (WGD) events that expanded gene families associated with alkaloid biosynthesis. Metabolomic analysis identified 4,456 metabolites, including 238 alkaloids, showing that flowers and fruits are primary organs for PL biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified the key gene PsHCT1 and multiple transcription factors linked to PL biosynthesis. Molecular docking and enzyme assays confirmed that PsHCT1 catalyzes the condensation of sinapoyl-CoA and 5,6-dihydropyridinone, with PsCCoAOMT completing PL biosynthesis. This study lays the groundwork for enhancing medicinal compound production.