A near telomere-to-telomere genome reveals yellow camellias evolution and flavonols biosynthesis

Yellow camellias, medicinal species within the Camellia genus that accumulate high levels of flavonols, have unclear evolutionary histories and poorly understood mechanisms of flavonol accumulation. Here, we present a gap-free, haplotype-phased genome assembly of Camellia longruiensis . Haplotype-specific genes showed marked differences in transposon content and expression levels compared with biallelic genes. We also observed tissue-specific shifts in allelic expression direction, indicating that dominant allelic effects regulate secondary metabolic pathways, including phenylpropanoid biosynthesis. Population genomic analyses revealed that yellow camellia accessions from China and Vietnam experienced a shared demographic bottleneck and diverged approximately 10,000 years ago. We also identified strong selective signals in genomic regions associated with flavonol biosynthesis, such as WRKY23 . Molecular experiments further demonstrated that WRKY23 promotes flavonol accumulation by activating FLS expression. This study provides valuable genomic resources for germplasm conservation and establishes a foundation for elucidating the genomic basis of metabolite biosynthesis, thereby informing gene-editing–based breeding strategies. • A gap-free, haplotype-phased genome assembly for Camellia longruiensis , a valuable genomic resource. • Real the demographic history of yellow camellias. • Elucidate the key regulatory mechanism of flavonol accumulation.