The telomere-to-telomere genome and comparative analysis from algae to higher plants reveal origin and evolution of biosynthesis of chlorogenic acid pathway and production in ramie ( <i>Boehmeria nivea</i> L.)

Abstract Chlorogenic acid is an important secondary metabolite in plants, and its antioxidant and antimicrobial activities confers its remarkable medical value. Ramie (Boehmeria nivea), an important fiber crop, riches numerous Chlorogenic acid in the root and leaf, making it used as a traditional Chinese medicinal herb and livestock feed. In this study, we report a high-quality telomere-to-telomere (T2T) and gap-free genome of ramie. The assembly length was approximately 344 Mb, with all 28 telomeres and 14 centromeres. A total of 25 853 genes were identified, 90.5% of which were achieved functional annotation. Based on the T2T genome, we investigated the origin and evolution of the chlorogenic acid biosynthesis pathway and its production using comparative genomic and phylogenetic analyses. Subsequently, we identified five potential key genes involved in its biosynthesis via transcriptomic and metabolomic analyses, and characterized the metabolic pathway of chlorogenic acid biosynthesis in ramie through protease activity assays. Our T2T assembly represents the complete reference of genome and provides a valuable resource for genome and genetic studies in ramie; the proposed metabolic pathway of chlorogenic acid biosynthesis provided a basis for the improvement of chlorogenic acid content in ramie breeding.