Chloroplast Genome Diversity and Molecular Evolution in Hypericaceae: New Insights from Three Species.

The Hypericaceae family, comprising nine genera and over seven hundred species, includes plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three species: , , and , and conducted comparative genomic analyses with related species. The chloroplast genome sizes were 152,654 bp, 122,570 bp, and 137,652 bp, respectively, with an average GC content of 37.9%. All genomes showed a quadripartite structure, with significant variations in IR regions (3231-26,846 bp). The total number of genes ranged from 91 to 129. SSRs were predominantly located in the LSC region, with mononucleotide repeats being dominant. Comparative analysis identified several hotspot regions, including , , , and in the LSC region and , , , and in the SSC region. Nucleotide polymorphism analysis revealed eight highly variable regions and eleven gene loci, providing potential molecular markers for species identification. Phylogenetic analysis indicated that and are closely related to , with and being closest relatives and as their sister species. These findings provide molecular tools for species identification and insights for conservation strategies of medicinal species.