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

Jun-Ho Song,Sungyu Yang,Inkyu Park,Byeong Cheol Moon

doi:10.3390/plants9020157

Jun-Ho Song, Sungyu Yang + Show 2 more

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https://doi.org/10.3390/plants9020157

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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.

Highlights

IntroductionChloroplast (cp) genomes range in size from 115–180 kb and exhibit a quadripartite structure consisting of two single copy, a large single copy (LSC) region, a small single copy (SSC) region, and two copies of an inverted (IR) region (IRa and IRb) [2,3]
Chloroplasts play an essential role in photosynthesis and carbon fixation [1]
The cp genomes of all three Actaea species were of high quality (Figure 1, Table 1)

Summary

Introduction

Chloroplast (cp) genomes range in size from 115–180 kb and exhibit a quadripartite structure consisting of two single copy, a large single copy (LSC) region, a small single copy (SSC) region, and two copies of an inverted (IR) region (IRa and IRb) [2,3]. The structure of the cp genome is highly conserved among plant species compared with that of nuclear and mitochondrial genomes [4]. Cp genomes exhibit maternal inheritance, facilitating the conservation of gene contents and genome structure [5,6]. The cp genome is widely used for species identification, molecular marker development, evolutionary analysis and high-resolution phylogenetic analysis [7,8,9]. Cp genome sequencing represents a viable alternative to DNA barcoding, a controversial method of species identification.

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