摘要Potato is the world's most important nongrain crop.In this study,to assess genetic diversity within the Pe-tota section,29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes,landraces,and modem cultivars were re-sequenced at＞25 × depth.Subse-quently,a graph-based pangenome was constructed using DM8.1 as the backbone,integrating194,330 nonredundant structural variants.To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits,LC-MS/MS was employed to obtain the metabolome of 157 accessions,and 9,321 structural variants(SVs)were detected to be significantly associated with 1,258 distinct metabolites via PAV(presence and absence variations)-based metabolomics-GWAS analysis,including metabolites of flavonoids,phenolic acids,and phospholipids.To facilitate the utilization of pangenome resources,a comprehensive platform,the Potato Pangenome Database(PPDB),was developed.Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato,which will accelerate functional genomics studies and genetic improvements in potato.