Comprehensive Comparative Analyses of Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny.

Limestone karsts are renowned for extremely high species richness and endemism. (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of species are mainly based on their specialized and diverse floral structures. plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of . In this study, we reported chloroplast (cp) genomes of seven species (, , , , , , and ). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of cp genomes. We identified eight divergent hotspot regions (-GCA-, -UUC-, , , , , and ) that serve as potential molecular markers. Our newly generated plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of species.