Pan-Plastome Analysis Reveals the Genetic Diversity and Genetic Divergence of Adenocaulon himalaicum (Asteraceae)

The pan-plastome approach provides a powerful tool for investigating intraspecific divergence and population genetics due to its unique advantages, including single-copy genes, absence of recombination, and moderate nucleotide substitution rates. <i>Adenocaulon himalaicum</i> Edgew. (Asteraceae), a widely distributed medicinal herb in East Asia, remains genomically understudied at the population level, with no comprehensive pan-plastome assembly available to date. Here, we de novo assembled pan-plastome of 87 individuals from 18 populations representing its known distribution range. The pan-plastome exhibited a typical quadripartite structure (152,129 bp to 152,207 bp), containing 113 unique genes, most of which were under purifying selection. Phylogenetic and haplotypes analyses revealed three distinct genetic lineages corresponding to their geographic distribution. Population genetic analyses showed significant differentiation among three genetic groups (AMOVA: 73.43% variation among groups) and a strong isolation-by-distance pattern (IBD: r = 0.469, <i>p</i> = 0.001). The pronounced population structure underscores the imperative for establishing distinct conservation units, with particular emphasis on marginal populations that may harbor unique genetic compositions and potential medicinal properties. Our study presents the first pan-plastome for <i>A. himalaicum</i>, offering new insights into its plastome evolution and population divergence, providing valuable genomic resources to guide future breeding and sustainable utilization of medicinal herbs.