The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

Abstract

Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC–trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.

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

“…The majority of divergent sequences were located in the IGS regions. In genic regions, matK, ycf1, and ycf2 showed greater divergence than other genes; this is consistent with previous studies [35][36][37]. The matK gene harbors an important DNA barcode region for species identification [35].…”

“…Additionally, A. biternata and A. asiatica showed high divergence in the region from petB to petD ( Figure 2). Divergence in the ndhC-trnV-UAC region, known as the hotspot region, has been detected in the cp genomes of other angiosperms [36,37]. These regions represent potential candidates for molecular marker development for species identification.…”

Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

“…Although the cp genome is generally conserved, it has undergone intraand inter-species rearrangement during evolution [10,11], including IR expansion and contraction. The information obtained from sequence rearrangements can be applied in phylogenetic analyses to solve taxonomic problems, such as low-level classifications, using genome comparison [12][13][14][15][16][17]. In the section Michelia, complete cp genomes have been reported for only Magnolia alba (NC037005), Magnolia laevifolia (NC035956), and Michelia odora (NC023239).…”

Complete chloroplast genome of Achyranthes bidentata Blume

“…Dried roots of A. bidentata, called Achyranthis Radix, are used as a Korean traditional herbal medicine to treat anti-arthritic, anti-allergic, anti-diuretic, and other diseases (Korea Institute of Oriental Medicine (KIOM) 2019). Unfortunately, other similar plant species are mixed with A. bidentata, a valuable herbal medicine, and indiscriminately misused in Korean herbal markets (Moon et al 2017). Thus, to accurately identify A. bidentata and discriminate it from other similar species, we sequenced its complete chloroplast genome.…”