Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name “Bang-poong”. We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5–6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2–3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species.

Curcuma longa, C. wenyujin and C. phaeocaulis are important herbal medicine which of rhizomatous herbaceous perennial plant of the family Zingiberaceae. This study generated a complete chloroplast genome sequence of three medicinal species were characterized by de novo assembly with whole genome sequencing data. The length of complete chloroplast genome were 162,180 bp ( C. longa ), 162,266 bp ( C. wenyujin ), and 162,133 bp ( C. phaeocaulis ), respectively, with four structures that were included in large single copy region (87,001 bp, 87,042 bp, and 87,013 bp), small single copy region (15,681 bp, 15,710 bp, and 15,622 bp), and duplicated inverted regions (29,749 bp, 29,757 bp and 29,749 bp of each). Based on phylogenetic trees, C. longa, C. wenyujin, and C. phaeocaulis were grouped by high bootstrap value with Curcuma species. This result approved that C. longa, C. wenyujin and C. phaeocaulis were comprised in Alpinia and Wurfbainia . Therefore, this chloroplast genome data firstly generated valuable genetic resource in discrimination of herbal materials, phylogeny and development DNA marker.

Angelica decursiva (Miquel) Franchet & Savatier (Apiaceae) has been used as a significant medicinal plant in East Asia. We determined its complete chloroplast genome for the first time in this study. The complete chloroplast was circularized and had a typical quadripartite structure genome of 146 719 bp long including the large single copy region (LSC) of 93 256 bp, the small single copy region (SSC) of 17 497 bp and duplicated inverted regions (IRs) of 17 983 bp each. The total GC content was 37.56% and for the four structures it was 35.98% (LSC), 31.06% (SSC), and 44.83% (for each IR). There were a total of 113 genes, comprising four rRNAs, 29 tRNAs and 80 protein coding genes. In the phylogenetic analysis, A. decursiva was grouped with Seseli montanum. This study may contribute to authenticating the plant’s correct use as medicine for health and provide an important genetic resource for phylogeny with related species.

Ostericum koreanum Kitagawa is an important herbal medicine, whose taxonomic status has been changed to Angelica reflexa as a new species. This study generated the complete chloroplast genome sequence of O. koreanum , and reconsidered its molecular taxonomic status in Angelic a by comparing it with related species. The length of the complete chloroplast genome was 147,282 bp, and there were four structures that included the large single copy region (93,185 bp), the small single copy region (17,663 bp) and the duplicated inverted regions (18,217 bp of each). Based on its phylogenetic trees, O. koreanum was grouped by high bootstrap value with the Angelica species. This result proved that O. koreanum is included in Angelica . Therefore, this chloroplast genome data generated for the first time a valuable genetic resource for the discrimination of herbal materials, phylogeny, and evolution.