Multi‐Omics Insights Into Anthraquinone Biosynthesis in <i>Rheum tanguticum</i>

Rheum tanguticum is renowned for its medicinal properties, including purgative, anti-inflammatory and hepatoprotective effects, primarily attributed to anthraquinones (AQs). However, the molecular mechanisms of AQs biosynthesis have largely been hindered by insufficient genomic resources and functional genomics investigations. Here, we employed multi-omics approaches to address this knowledge gap. The high-quality T2T-level genome was constructed with a size of 2.68 Gb and a contig N50 of 233.65 Mb. Functional annotation revealed that the specific and expanded gene families of R. tanguticum are involved in efficient energy metabolism and secondary metabolite biosynthesis, providing a molecular basis for its stress adaptation and medicinal value. Integrated widely targeted metabolomics, spatial metabolomics and targeted quantification of AQs, we successfully elucidate the AQs spatiotemporal accumulation patterns. Seeds and leaves are key sites for the synthesis and transport of free AQs, while the root core serves as the primary location for the synthesis and accumulation of conjugated AQs. Through integrated genomic, transcriptomic, metabolomic and functional validation analyses, we preliminarily characterised the positive regulatory role of RtPKSIII-8 in the synthesis of aloe-emodin and emodin, as well as the potential function of RtUGT85AD11 in the biosynthesis of AQs and flavonoids. These findings provide essential genomic and functional data for deciphering AQs biosynthetic pathways and lay a theoretical foundation for the medicinal development and genetic improvement of R. tanguticum.