The Hypericaceae family, comprising nine genera and over seven hundred species, includes Hypericum plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three Hypericum species: Hypericum acmosepalum, Hypericum addingtonii, and Hypericum beanii, 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 accD, rpoC2, rpoB, and rpl22 in the LSC region and matK, rpl32, rpl33, and rps4 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 Triadenum and Cratoxylum are closely related to Hypericum, with H. acmosepalum and H. beanii being closest relatives and Hypericum hookerianum as their sister species. These findings provide molecular tools for species identification and insights for conservation strategies of medicinal Hypericum species.

Genomic analysis is crucial for understanding the evolutionary history, phylogenetic relationships, and effective conservation of plant species. Casearia kurzii is an important medicinal plant of the genus Casearia, but its complete chloroplast genome has not previously been reported, limiting genetic studies and conservation efforts. In this study, we assembled and annotated the complete chloroplast genome of C. kurzii using Illumina sequencing technology and conducted a comparative genomics analysis with 14 closely related species to clarify its phylogenetic position within Casearia. The chloroplast genome was 157,998 bp, showing a typical quadripartite structure. Key findings included: (1) the loss of the rpl22 gene at the IR boundary; (2) the identification of 60 simple sequence repeats (SSRs) and (3) the discovery of five candidate molecular markers for species-level identification. Phylogenetic analysis revealed that C. kurzii formed a strongly supported monophyletic clade (100% bootstrap support) with C. velutina, C. decandra, and C. glomerata, this clade originated approximately 15.8 million years ago. This study provides molecular tools for accurate identification and conservation of C. kurzii and related species, laying the foundation for exploring adaptive evolution within Casearia and advancing comparative genomics research.