Extreme plastome conservation and adaptive evolution study in the medicinal plant Aralia elata (Araliaceae)

This study presents a comprehensive analysis of the chloroplast genome of the medicinal plant Aralia elata . We sequenced and annotated a plastome from Central China and integrated it with 17 published plastomes representing nearly the entire Chinese distribution range of the species. Our objectives were to characterize plastome evolution, reconstruct intraspecific phylogeny, and identify divergent hotspots and genes under selection. Results revealed extreme structural conservation across all plastomes, evidenced by invariant quadripartite architecture, stable GC content, conserved IR/SC boundaries, gene collinearity, and codon bias. Despite this stability, we identified ten hypervariable regions (e.g., ycf1 , clpP ) as novel molecular markers for future intraspecific and population genetic studies. Positive selection was identified in the plastid gene rps12 , which may reflect adaptation to environmental heterogeneity. This work provides crucial genomic resources and insights, establishing valuable markers for species identification, population genetics, and informing conservation strategies for A. elata .