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. 2021 Dec 28;7(1):115–117. doi: 10.1080/23802359.2021.2011448

The complete chloroplast genome of Aconitum piepunense (Ranunculaceae) and its phylogenetic analysis

Xueshan Ni a,b, Jian Li a, Yunfei Li a, Haizhu Zhang a,b, Baozhong Duan a,b, Xubing Chen a,b, Conglong Xia a,b,✉
PMCID: PMC8725895  PMID: 34993331

Abstract

Aconitum piepunense belonging to the family Ranunculaceae is an endangered herb species in southwestern China. In this study, the complete chloroplast genome of A. piepunense was sequenced, and the results revealed a typical quadripartite structure with a length of 155,836 bp, including a large single-copy region (LSC, 86,433 bp), a small single-copy region (SSC, 16,945 bp), and a pair of inverted repeat (IR) regions (IRa and IRb, 26,229 bp, respectively). A total of 130 genes were identified in the A. piepunense chloroplast genome, containing 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis based on the maximum likelihood method indicated that A. piepunense formed a monophyletic group, which was sister to A. contortum and A. vilmorinianum.

Keywords: Aconitum piepunense, complete chloroplast genome, phylogenetic analysis

The genus Aconitum includes approximately 400 species that belong to the Ranunculaceae family (Park et al. 2017). Even though Aconitum possesses substantial toxicity, it is one of the most significant medicinal plants globally (Li and Kadota 2001). Modern pharmacological studies have shown that Aconitum has various pharmacological effects, especially analgesic and anti-inflammatory activities (Zhou et al. 2015). Aconitum piepunense is a critical medicinal plant, mainly distributed in tropical areas with an altitude of around 3000 m. At least sixteen active compounds of this species were discovered in the previous studies (Cai, Chen, Liu, et al. 2006; Cai, Chen, Liu 2006; Cai et al. 2010). Due to the apparent pharmacological activities, wild resources of A. piepunense are on the verge of extinction. Given this situation, to unravel the complete chloroplast genome of A. piepunense would pave the way for its molecular authentication and resource conservation.

Fresh leaves of A. piepunense were collected from the Alpine Botanical Garden, Zhongdian County, Yunnan Province, China (99°63′29″E, 27°91′62″N) and dried with silica gel. The plant specimen was deposited in the herbarium of Dali University, under the voucher number ZD201909. Total genomic DNA was extracted using a plant DNA kit (OMEGA, Shanghai, China). Approximately 1 ng of DNA was used to construct the library with a DNA sample preparation kit (Illumina Inc., San Diego, CA, USA). The library was sequenced on an Illumina NovaSeq platform at 2 × 150 bp using the Trusrq SBS Kit (Illumina Inc., San Diego, CA, USA). The obtained raw data were filtered using Trimmomatic v0.39 to ensure the accuracy of the following assembly results (Bolger et al. 2014). The chloroplast genome of A. piepunense was assembled using Novoplasty 4.0 (Dierckxsens et al. 2017), and the A. contortum chloroplast genome (NC038098) was used as the reference. To explore the phylogenetic relationship of A. piepunense, 26 complete chloroplast genomes were downloaded from Genbank (https://www.ncbi.nlm.nih.gov/). All chloroplast sequences were aligned using MAFFT v7 (Katoh and Standley 2013). The maximum likelihood (ML) method was adopted to construct a phylogenetic tree using MEGA X (Kumar et al. 2018) based on 1,000 replicates and the best-fit nucleotide model TVM + F + R4. The complete chloroplast genome sequence of A. piepunense was submitted to GenBank under the accession number MZ169393.

The chloroplast genome of A. piepunense was 155,836 bp in length and showed a typical quadripartite structure, including a large single-copy region (LSC, 86,433 bp), a small single-copy region (SSC, 16,945 bp), and a pair of inverted repeat (IR) regions (IRa and IRb, 26,229 bp, respectively). In addition, the coding regions (78,342 bp) accounted for 50.27%, while the intergenic regions (77,494 bp) accounted for 49.73%. The total GC content of this chloroplast genome was 37.8%. A total of 130 genes were annotated, containing 85 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes.

The ML tree showed that A. piepunense formed a monophyletic group that was sister to A. contortum and A. vilmorinianum; all the three species belonged to the subgenus Aconitum. It is worth mentioning that Gymnaconitum gymnandrum clustered into a clade with Delphinium grandiflorum, and sistered to the other three Delphinium species (Figure 1). The ML tree revealed a deep-level phylogenetic relationship of A. piepunense. These results contribute to the phylogeny and molecular authentication of this traditional medicinal plant.

Figure 1.

Figure 1.

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Phylogenetic relationships of the 27 species inferred from maximum likelihood (ML). The bootstrap value shown on each node was obtained based on 1000 replicates.

Funding Statement

This work was supported by the Major Science and Technology Project in Dali Prefecture [D2019NA03].

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/) under the accession MZ169393. The associated BioProject, SRA, and Bio-Sample ID are PRJNA748565, SRR15206984, and SAMN20338565, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/) under the accession MZ169393. The associated BioProject, SRA, and Bio-Sample ID are PRJNA748565, SRR15206984, and SAMN20338565, respectively.

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