Complete Chloroplast Genomes of Three Wild Perennial Species from Central Asia: Genome Structure, Mutation Hotspot, Phylogenetic Relationships, and Comparative Analysis

L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial species, including , , and , have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of showed certain sequence variations compared with the cp genomes of the other two species ( and ), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three species. A series of hotspots regions (- ~ -, - ~ , ~ , ~ , etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (, , , , and ) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of L. This study offers a framework for gaining a better understanding of the evolutionary history of species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.