Telomere-to-telomere genome assembly of yellow-fruited allotetraploid American ginseng ( Panax quinquefolius L . ) provides insights into flavonoid biosynthesis

Abstract Panax quinquefolius L., commonly known as American ginseng, is a valuable beneficial medicinal herb renowned for its health-promoting properties and rich phytochemical profile. Despite significant progress in understanding ginsenoside biosynthesis, the genetic basis for flavonoid diversity in American ginseng remains unclear. This study reports the first telomere-to-telomere (T2T) genome assembly for yellow-fruited American ginseng cultivar ‘Zhongnongyangshen No. 2’. The genome assembly, achieved using PacBio HiFi and Oxford Nanopore Technology ultra-long read technologies, offers a high-quality reference for genomic research, addressing previous gaps in structural accuracy. Combining transcriptomic and metabolomic analyses, we investigated flavonoid biosynthesis and the regulatory mechanisms underlying fruit color variation during different developmental stages of American ginseng. Our findings highlight the phylogenetic evolution of the American ginseng genome and offer new insights into the biosynthetic pathways of anthocyanins and flavonols. This comprehensive genomic resource facilitates deeper exploration of flavonoid diversity, supports genetic improvement efforts, and enhances the potential for future applications in medicinal plant research.