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. 2021 Feb 8;6(2):327–328. doi: 10.1080/23802359.2020.1866453

The complete chloroplast genome sequence of medicinal plant: Dianthus chinensis (Caryophyllaceae)

Zhen Yang a, Xuhang Wang b, Dong Wang a, Panpan Xue a, Ning Miao a,✉
PMCID: PMC7872571  PMID: 33659666

Abstract

Dianthus chinensis is a medicinal plant. Its complete chloroplast genome sequence is 149,570 bp in length, containing 126 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 34 tRNA genes (34 tRNAs). The overall GC content of cp DNA is 34.1%, the corresponding values of the LSC, SSC, and IR regions are 34.0%, 29.8%, and 42.5%, respectively. Phylogenetic tree shows that D. chinensis is a sister to D. longicalyx.

Keywords: Chloroplast genome, phylogenetic analysis, Caryophyllaceae, Dianthus chinensis

The Dianthus genus consists of nearly 300 species native to Europe and Asia (Czerepanov 1973; Tang and Lu 1996). The blooms of Dianthus chinensis Linnaeus are five petaled. The petals are deeply notched, giving them a feathery or fringed appearance. D. chinensis is used as a popular garden plant over 2000 years. It is taken internally to treat acute urinary tract infections, urinary stones, constipation and failure to menstruate (Wang et al. 1998). It is applied externally to treat skin inflammation and swelling. The leaves are used in the treatment of hemorrhoids, lumbricoid worms, and venereal sores, while the flowers are used as an astringent, diuretic, hemostatic, resolvent, and vulnerary (Shin et al. 2012). However, the chloroplast genome of D. chinensis has not been reported. In this study, we assembled the complete chloroplast genome of D. chinensis, hoping to lay a foundation for further research.

Fresh leaves of D. chinensis were collected from Haiyuan (Zhongwei, Ningxia, China; coordinates: 105°37′E, 36°12′N) and dried with silica gel. The voucher specimen was stored in Sichuan University Herbarium with the number QTPLJQ14383118. Total genomic DNA was extracted with a modified CTAB method (Doyle and Doyle 1987) and a 350-bp library was constructed. This library was sequenced on the Illumina NovaSeq 6000 system with 150 bp paired-end reads. We obtained 10 million high-quality pair-end reads for D. chinensis, and after removing the adapters, the remaining reads were used to assemble the complete chloroplast genome by NOVOPlasty (Dierckxsens et al. 2017). The complete chloroplasts genome sequence of D. longicalyx was used as a reference. Plann v1.1 (Huang and CronK 2015) and Geneious v11.0.3 (Kearse et al. 2012) were used to annotate the chloroplasts genome and correct the annotation.

The total plastome length of D. chinensis (MT712072) is 149,570 bp, exhibits a typical quadripartite structural organization, consisting of a large single-copy (LSC) region of 82,981 bp, two inverted repeat (IR) regions of 24,748 bp and a small single-copy (SSC) region of 17,093 bp. The cp genome contains 126 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 34 tRNA genes (34 tRNAs). Most genes occur in a single copy, while 15 genes occur in double, including all rRNAs (4.5S, 5S, 16S, and 23S rRNA), 7 tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 4 PCGs (rps7, ndhB, ycf2, rpl2). The overall GC content of cp DNA is 36.3%, the corresponding values of the LSC, SSC, and IR regions are 34.0%, 29.8%, and 42.5%, respectively.

In order to further clarify the phylogenetic position of D. chinensis, plastome of nine representative Dianthus species were obtained from NCBI to reconstruct the plastome phylogeny, with Psammosilene tunicoides as an outgroup. All the sequences were aligned using MAFFT v.7.313 (Katoh and Standley 2013) and maximum likelihood phylogenetic analyses were conducted using RAxML v.8.2.11 (Stamatakis 2014) under GTRCAT model with 500 bootstrap replicates. The phylogenetic tree shows that Dianthus were divided into two subclades. Dianthus caryophyllus, D. moravicus, and D. gratianopolitanus cluster together. Other species cluster in another clade, while D. chinensis is a sister to D. longicalyx (Figure 1).

Figure 1.

Figure 1.

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Phylogenetic relationships of Dianthus species using whole chloroplast genome. GenBank accession numbers: Dianthus caryophyllus (KU904222), Diathus chinensis (MT712072), Dianthus gratianopolitanus (LN877395), Dianthus longicalyx (KM668208), Dianthus moravicus (LN877396), Psammosilene tunicoides (MH521155).

Funding Statement

This study was supported by the China’s National Natural Science Foundation [31770490].

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference number MT712072.

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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 data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference number MT712072.

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