Population transcriptomic and metabolomic profiling provide novel insights into evolutionary mechanisms of metabolomic diversity between divergent lineages of Rheum palmatum complex.

The quality of traditional Chinese medicine (TCM) greatly relies on the accumulation of medicinal compounds. As a crucial TCM, rhubarb (dahuang) exhibits significant quality variations across different geographical production regions. However, the insufficient knowledge on metabolic diversity and metabolic pathways of specialized metabolites across distinct geographical regions fundamentally constrains our ability to decipher the mechanisms driving quality differences among different production areas in rhubarb. Here, we infer the evolutionary mechanisms underlying metabolomic diversity of the rhubarb source plants (Rheum palmatum complex) using population transcriptomic and metabolomic analyses. Our findings revealed that there were three distinct lineages within the complex. The divergence of eastern and western lineages could be dated back to ~2.31 million years ago (Mya), while the split between NW and SW lineages in western China occurred ~1.64 Mya. Gene expression analysis revealed comparable distribution proportions of highly expressed and lowly expressed genes among populations, while divergence in expression diversity was observed between specific lineages. Untargeted metabolomic analyses detected 819 differentially accumulated metabolites in different genetic lineages. Subsequent analysis uncovered potential associations between genetic variants and the accumulation of medicinal compounds. Notably, four PKSs, among which RpALSs were included, demonstrated a high degree of connectivity with other genes involved in anthraquinone and stilbene biosynthesis. Additionally, we found that one UGT was involved in the biosynthesis of sennoside A through mGWAS. Our results provide valuable insights into the quality variation of rhubarb and establish a solid foundation for future research and development endeavors.