Phylogenetic relationship and characterization of the complete chloroplast genome of the Coriaria nepalensis Wall. in China, a least concern folk medicine

Abstract

Coriaria nepalensis Wall. is a toxic Chinese herbal medicine. In this study, the complete chloroplast (cp) genome of C. nepalensis was first reported. The length of the large single-copy (LSC) region was 158,499 bp, the small single-copy (SSC) region was 18,411 bp, and the inverted repeats (IRs) region were 26,552 bp, with 37.76% overall GC content. There were 132 genes in total, including 86 mRNA, 38 tRNA, and 8 rRNA. Phylogenetic analysis showed that C. nepalensis was closely related to Corynocarpus laevigatus.

Keywords:

• Coriaria nepalensis
• complete chloroplast genome
• phylogenetic analysis

Coriaria nepalensis Wall. is a shrub belonging to single-genus of Coriaria (Coriariaceae family), and mainly distributed in the southern and southwestern of China. It is commonly used for the treatment of numbness, toothache, traumatic injury, and acute conjunctivitis in traditional Bai folk medicine (Jiang and Duan 2014), which are toxic to many animals (Wang et al. 2016). Previous studies on C. nepalensis mainly focused on chemical components and biological characteristics (Wang et al. 2016; Zhao et al. 2018). However, the complete chloroplast (cp) genome sequence of C. nepalensis has not been reported so far. Herein, we assembled and characterized the cp genome of C. nepalensis for the first time. Besides, its phylogenetic relationship with several plant species was investigated, which will provide significant genomic information to study the evolution of the Coriariaceae.

Fresh leaves of C. nepalensis were collected from the Cangshan mountain (25°67′30″N, 100°15′72″E) of Dali counties, Yunnan province, China. The voucher specimen was deposited in the herbarium of Dali University (LJ2020010506). Total DNA was extracted using the DNeasy plant mini kit (QIAGEN), and sequenced by Illumina NovaSeq system (Illumina, San Diego, CA, USA). About 8.05 Gb of raw data with 53,700,486 paired-end reads were assembled by NOVOPlasty (Dierckxsens et al. 2017; Park et al. 2019), and the assembled cp genome was annotated by GeSeq with default sets (Michael et al. 2017; Qian et al. 2020). The annotated cp genome of C. nepalensis was submitted to the GenBank with the accession number of MT106774.

The cp genome of C. nepalensis was 158,499 bp in length, with a typical quadripartite structure of large single-copy (LSC) region of 86,984 bp, and a small single-copy (SSC) region of 18,411 bp, separated by a pair of inverted repeats (IRs) region of 26,552 bp. It contained 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA. The overall GC content was 36.76%. To confirm the phylogenetic relationship of C. nepalensis, a phylogenetic analysis was performed based on 20 cp genomes. Meanwhile, two species from the Aristolochiaceae (Aristolochia debilis and Aristolochia contorta) were used as outgroups. The sequence was aligned by MAFFT v7.307 (Katoh and Standley 2013), and then a neighbour-joining (NJ) tree was constructed using MEGA 6.0 (Tamura et al. 2013) with 1000 bootstrap replicates. The result showed that C. nepalensis was closely related to Corynocarpus laevigatus (Figure 1). In total, this study reports the first cp genome of species in Coriariaceae which would be beneficial to potential studies on phylogenetics of the genus and related group in Coriariaceae.

Figure 1. Neighbor-joining (NJ) tree based on the cp genome of 21 species with Aristolochiaceae as an outgroup. The bootstrap values were 1000 replicates.

Disclosure statement

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

Additional information

Funding

This work was supported by the Cultivating Plan Program for the Leader in Science and Technology of Yunnan Province [2015HB058], the key technology project in Yunnan province of China [No. 201800501], and the Innovation Team project for traditional Chinese medicine resources and ethnic medicine of Dali University [ZKLX2019318].