Abstract

Phoebe zhennan is an endangered and endemic tree species in China, renowned for its distinctive “golden-thread nanmu” wood with exceptional economic, ecological, and cultural value. However, the molecular basis underlying this unique wood trait remains poorly understood. Here, we report a telomere-to-telomere genome assembly of P. zhennan , spanning 919.42 Mb with a contig N50 of 84.44 Mb. Integrated metabolomic analyses identify morin, a flavonol compound, as a major contributor to the “golden-thread” phenotype. Functional characterization through enzymatic assays and transient overexpression reveals that PzF3′HL plays a central role in morin biosynthesis. Transcriptomic and single-nucleus RNA sequencing (RNA-seq) analyses further demonstrate age-dependent and xylem-specific activation of flavonoid pathway genes, driving flavonoid accumulation. Additionally, we reconstruct potential regulatory networks involved in flavonoid biosynthesis in P. zhennan stems. These findings provide critical insights into the genetic and biochemical mechanisms of “golden-thread nanmu” formation, offering valuable resources for the conservation and molecular breeding of P. zhennan .