Resolving taxonomic complexities in medicinal Aralia: Genome-scale phylogeny and super-barcoding advance species identification and conservation

Aralia section Dimorphanthus represents the largest section in Araliaceae and has been employed in East Asian traditional medicine for centuries. However, the morphological complexity and the prevalence of hybridization/introgression posed a great challenge for accurate species identification, thereby hindering the development, conservation and application of these medicinal plants. In this study, we employed sequences of hundreds of nuclear loci and the complete plastomes to reconstruct the phylogenetic relationships, and evaluated the effectiveness of 12 distinct barcode systems for distinguishing Chinese species of Aralia sect. Dimorphanthus. We found that plastome length, gene content, and order of these species were highly conserved, while the inverted repeat regions showed variability between temperate and tropical/subtropical lineages, providing novel markers for geographical traceability. Phylogenetic relationships constructed based on the genome-scale data confirmed that Chinese Aralia sect. Dimorphanthus was monophyletic and comprised three well-supported lineages. Incomplete lineage sorting and hybridization were identified as the main factors contributing to the phylogenetic conflicts among trees. Species discrimination analysis revealed that super-barcoding strategies integrating complete plastomes and nrDNA sequences, achieved a 92 % species identification accuracy among the 14 studied species of Aralia sect. Dimorphanthus, outperforming standard barcodes. While this system resolved most taxonomic ambiguities, the inclusion of universal nuclear markers is crucial to resolve ambiguities in highly variable taxa like A. elata. These advancements directly support industrial needs for reliable species authentication and biodiversity conservation in pharmacologically important species.