The complete chloroplast genome of Aconitum puchonroenicum Uyeki & Sakata (Ranunculaceae), a rare endemic species in Korea

Abstract

The chloroplast genome sequence of Aconitum puchonroenicum Uyeki & Sakata, a rare endemic species in Korea, was characterized through de novo assembly with next-generation sequencing data. The chloroplast genome is 155,631 bp in length and contains 4 rRNA genes, 29 tRNA genes, and 78 protein-coding genes. Phylogenetic analysis demonstrated a close relationship of A. pseudolaeve with other species belonging to Aconitum subgn. Lycoctonum in Ranunculaceae.

Keywords:

• Aconitum puchonroenicum
• chloroplast genome
• Ranunculaceae
• phylogenetic analysis

Aconitum puchonroenicum Uyeki & Sakata belongs to the Aconitum subgn. Lycoctonum (Ranunculaceae), and is a rare endemic species of Korea (Uyeki and Sakata 1938). It was firstly described by Uyeki and Sakata (1938) from Puchon plateau and Birobong peak of Mt. Geumgang in northern Korea mainly on the basis of its inflorescence shape. According to the original description, A. puchonroenicum is clearly distinguished from the remaining taxa of the subgn. Lycoctonum by having elongated pedicels, glabrous stem, and smooth straight hairs on pedicel, carpel and sepal (Uyeki and Sakata 1938; Im and La 1996). Since Uyeki and Sakata’s first description (1938), the species has been known to be restricted to the northern part of the Korean Peninsula by most Korean botanists (Im and La 1996; Park et al. 2007). During several field works in Gangwon-do, South Korea, the second author collected this poorly unknown species and recognized that it is distinguished from the remaining taxa of subgn. Lycoctonum with yellow-flowers in Korea. A few populations are newly discovered in shady habitats with rich soils along the ridges of high mountains more than alt. 1400 m in Gangwon-do, South Korea. In particular, it has extremely narrow ranges in distribution and its population is very limited. To date, since there are only a few populations recorded in South Korea, this species is facing a very high risk to extinction in the wild in the near future.

In this study, we characterized the complete chloroplast genome sequence of A. puchonroenicum which will contribute to the further studies on its population genetics and further phylogenetics of Aconitum subgn. Lycoctonum. The specimen was collected from Taebaek-si (37°09′16.8″N, 128°55′4.6″E), Gangwon-do, South Korea, and deposited at the herbarium of National Institute of Biological Resources (KB) with the accession number NIBR-VP0000592796. Illumina Sequencing was conducted by MiSeq platform (Illumina Inc., San Diego, CA) and high-quality paired-end reads of ca. 1.58 Gb were assembled into a circular DNA (GenBank Accession no. MN967020).

The chloroplast genome of A. puchoroenicum is 155,631 bp in length (GC content is 38.05%) and has a typical quadripartite structure: 86,689 bp of a large single-copy (LSC) and 17,088 bp of a small single-copy (SSC) regions are separated by 25,927 bp of a pair of inverted repeat (IR) regions. It contains a total of 111 genes (4 rRNA genes, 29 tRNA genes, and 78 protein-coding genes), of which 19 genes (4 rRNAs, 7 tRNAs, and 8 protein-coding genes) are duplicated in IR regions.

To understand its phylogenetic relationship of A. puchonroenicum with relative taxa, a maximum likelihood (ML) tree was constructed using commonly conserved 78 protein-coding genes of 18 species in genus Aconitum and two outgroup species (Delphinium ceratophorum and D. anthriscifolium) (Figure 1). The ML tree showed that three subclades were circumscribed; these include (1) 9 species in subgn. Aconitum, (2) 8 species in subgn. Lycoctonum, (3) monotypic species in subgn. Gymnaconitum (Figure 1) in congruence with a previous phylogenetic analysis of Aconitum (Kadata 1987; Wang 1979; Li 2001). In addition, A. puchonroenicum was grouped with A. angustius, A. longecassidatum, A. finetianum, and A. pseduolaeve belonging to the sect. Lycoctonum ser. Volubilia (Hong et al. 2017), having a close relationship with A. pseudolaeve (Figure 1). The complete chloroplast genome of A. puchonroenicum will provide a valuable resource for the interspecific relationships in subgn. Lycoctonum as well as for the phylogenetic studies of Aconitum.

Figure 1. Maximum-likelihood(ML) tree based on the 78 chloroplast protein-coding genes of 20 taxa including A. puchonroenicum. These sequences were aligned using MAFFT (http://mafft.cbrc.jp/alignment/server/index.html) and used to generate ML phylogenetic tree by MEGA 7.0 (Kumar et al. 2016). The scale bar denotes the number of changes over the whole sequences. NCBI accession numbers are in parentheses.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by a grant from the National Institute of Biological Resources, the Ministry of Environment, Korea [NIBR201922101].