Abstract
Stephania kwangsiensis (Menispermaceae) is a rare and critically endangered species endemic to China. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 156,624 bp, which contained inverted repeats (IR) of 24,348 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,759 bp and 20,169 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two processed pseudogenes. The overall GC content of the plastome is 38.4%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that S. kwangsiensis is related to the congeneric S. japonica.
Keywords: Stephania, chloroplast genome, phylogenetic analysis
Stephania kwangsiensis H. S. Lo., a perennial deciduous herbaceous liana which belongs to the family Menispermaceae, is a rare and critically endangered species endemic to China. It is limited distributed throughout the Guangxi Zhuang Autonomous Region and Yunnan Province of China (Min and Zhong 1980). However, because of the limited population and narrow distribution area, S. kwangsiensis is treated as rare and endangered species in China and has been registered on the China Species Red List (Fu 1991). It is thus urgent to take effective measures to conserve this critically endangered and precious species. Herein, we first report and characterize the complete plastome of S. kwangsiensis based on Illumina paired-end sequencing data, which will contribute to the further studies on its genetic research and resource utilization. The annotated cp genome of S. kwangsiensis has been deposited into GenBank with the accession number MN654112.
In this study, S. kwangsiensis was sampled from in Guangxi Zhuang Autonomous Region of China, located at 110°21′34″ E, 22°47′11″ N. A voucher specimen (Y.-C. Shi et al. H1128) was deposited in the Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China. The experiment procedure is as reported in Zhang et al. (2019). Around 2 Gb clean data were used for the cp genome de novo assembly by the program NOVOPlasty (Dierckxsens et al. 2017) and direct-viewing in Geneious R11 (Biomatters Ltd., Auckland, New Zealand). Annotation was performed with the program Plann (Huang and Cronk 2015) and Sequin (http://www.ncbi.nlm.nih.gov/).
The chloroplast genome of S. kwangsiensis is a typical quadripartite structure with a length of 156,624 bp, which contained inverted repeats (IR) of 24,348 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,759 bp and 20,169 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two processed pseudogenes. Among the annotated genes, 15 of them contain one intron (atpF, ndhA, ndhB, rps16, rpoC1, petB, petD, rpl16, rpl2, trnA-UGC, trnI-GAU, trnG-GCC, trnK-UUU, trnL-UAA, and trnV-UAC), and three genes (clpP, rps12, and ycf3) contain two introns. The overall GC content of the plastome is 38.4%.
To identify the phylogenetic position of S. kwangsiensis, phylogenetic analysis was conducted. A neighbor-joining (NJ) tree with 1000 bootstrap replicates was inferred using MEGA version 7 (Kumar et al. 2016) from alignments created using the MAFFT (Katoh and Standley 2013) using plastid genomes of 17 species. It showed the position of S. kwangsiensis is related to the congeneric S. japonica (Figure 1). Our findings can be further used for population genomic and phylogenomic studies of Menispermaceae. It will also provide fundamental data for the conservation, utilization, and management of this rare species.
Figure 1.
NJ phylogenetic tree of S. kwangsiensis with 17 species was constructed by chloroplast plastome sequences. Numbers on the nodes are bootstrap values from 1000 replicates. Michelia odora was selected as outgroups.
Funding Statement
This work was financially supported by Basic Business Expenses Project of Guangxi Institute of Botany [Guizhiye 19004].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fu LG. 1991. Red book of Chinese plants: rare and endangered plants. Beijing (China): Science Press. [Google Scholar]
- Huang DI, Cronk Q. 2015. Plann: a command-line application for annotating plastome sequences. Appl Plant Sci. 3(8):1500026. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis Version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Min Z, Zhong S. 1980. Studies on the alkaloids of Stephania kwangsiensis H. S. Lo. Acta Pharmacol Sin. 15:532–537. [PubMed] [Google Scholar]
- Zhang Y, Shi YC, Duan N, Liu BB, Mi J. 2019. Complete chloroplast genome of Euphorbia tirucalli (Euphorbiaceae), a potential biofuel plant. Mitochondrial DNA B. 4(1):1973–1974. [Google Scholar]