Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Abstract

Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.

Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae)

“…Complete cp genomes provide sufficient information to study the phylogenetic relationships among plants, including at low taxonomy level and for unresolved taxa (Jansen et al, 2007;Park et al, 2019Park et al, , 2020. ITS and cp loci have confirmed the correct classification of numerous Boraginaceae species and inference of their evolutionary relationships based on morphological characteristics (Cohen, 2014).…”

Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology

“…Plastid genome (i.e., plastome) sequences are valuable genomic resources for estimating phylogenetic relationships, particularly among closely related species and unresolved taxa 4 , 27 , 31 . The systematics of Korean irises have been widely discussed, and several molecular studies based on single molecular markers (e.g., psbA-trnH , trnL-F ) and plastome structure have been performed in the past 33 , 92 .…”

“…Plastome sequencing can be useful for species classification and identification and high-resolution phylogenetic analysis 27 , 28 . Facilitated by next-generation sequencing (NGS), plastome data are increasingly utilized for the investigation of phylogenetic relationships and for the development of DNA barcode markers for low-taxonomic-level identification and the discrimination of controversial taxa 29 – 31 . However, even though complete plastome data are available for a variety of Korean irises 32 , 33 , neither the detailed comparative analysis of Iris plastomes nor the combination of such analysis with micromorphological analysis has been conducted in the genus Iris as it has been in other taxonomic groups 34 – 36 .…”

Exploration of the Species-specific Dna Markers Based on the Complete Chloroplast Genome for Discriminating Curcuma Comosa Roxb. From Curcuma Latifolia Roscoe and Other Related Species

“…In our study, three regions, ndhA, trnT-trnL, and ndhC-trnV, were successfully de ned as species-speci c DNA markers for C. comosa. In previous publications, these same three regions were recommended for the identi cation of plants in the genera Dendrobium 50 , Actaea 31 , and Entandrophragma 28 . Then, nineteen crude drug samples claimed to be "Wan Chak Motluk" (C. comosa or C. latifolia) purchased from different herbal markets (Table S8) were examined using our developed species-speci c DNA markers, including ndhA, trnT-trnL, and ndhC-trnV regions (Figure S1; Table S9).…”