Comprehensive analysis of the pan-plastome in Panax: implications for interspecies divergence and shade tolerance

BACKGROUND: Panax, including medicinally important species such as P. ginseng, P. quinquefolius, and P. notoginseng, exhibits diverse pharmacological properties. However, morphological traits are lost and DNA is often degraded during processing, complicating species identification. As photosynthetic organelles, plastomes offer both stable molecular markers and a direct window into light adaptation. Unlike their sun-loving relatives (Aralia), Panax species are shade-tolerant, making them ideal for studying shade adaptation. RESULTS: Here, a total of 188 plastomes from Panax and its close relatives were annotated and analyzed, including 31 newly assembled plastomes of P. quinquefolius from diverse geographic regions. Through a deep comparative genomic analysis, we obtained the following findings: (1) Panax plastomes are highly conserved, with only minor shifts at IR-SC boundaries, and 3,397 variants identified across species. (2) All individuals of P. ginseng, P. quinquefolius, and P. notoginseng formed monophyletic clades, and two species-specific SNP markers were identified for accurate discrimination of these three key medicinal taxa. (3) Nine plastid genes showed significantly different selection patterns between Panax and Aralia, with intensified selection likely linked to shade adaptation. CONCLUSION: This study provides two single-nucleotide markers for authenticating processed medicinal materials and reveal plastome-level signatures of shade adaptation, offering valuable resources for species identification, cultivation and management.