Abstract
Clinopodium chinense is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of C. chinense to investigate its phylogenetic relationship in the family Labiatae. The chloroplast genome of C. chinense was 151,989 bp in length with 37.8% overall GC content, including a large single copy (LSC) region of 83,189 bp, a small single copy (SSC) region of 17,642 bp and a pair of inverted repeats (IRs) of 25,579 bp. The cp genome contained 113 genes, including 80 protein coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Clinopodium was closely related to Mentha.
Clinopodium L. is a genus of the Labiatae family, which includes 20 species. Most of them are widely distributed in Europe, Central Asia and Eastern Asia. There are 11 species in China (Li and Ian C Citation1994). Plants of this genus have been widely used in traditional Chinese medicine for thousands of years (Jiangsu New Medical College Citation1977). Among these species, C. chinense is widely distributed in southwest China which have been used in ethnic medicine for treatment of colds, hepatitis, enteritis, dysentery, mumps, mastitis, allergic dermatitis and conjunctivitis (Minru and Yi Citation2016). However, up to now for such medicinal plant, many studies have mainly focused on describing its chemical compositions (Ling-Tian et al. Citation2017) and pharmacognostic studies (Yin-Di Zhu et al. Citation2018; Shi Xiaoji et al. Citation2019; Yu Yingli et al. Citation2019), with little involvement in its molecular biology, so that no comprehensive genomic resource is conducted for it. Here, we report the chloroplast genome sequence of C. chinense and find its internal relationships within the family Labiatae.
Fresh and clean leave materials of C. chinense were collected from Lijiang city, Yunnan, China (N27°00′44.48″/E100°14′42.38″), and the plant materials and a voucher specimen (TC24) were deposited at Tourism and Culture College of Yunnan University (Lijiang). Total genomic DNA was extracted using the improved CTAB method (Doyle Citation1987; Yang et al. Citation2014), and sequenced with Illumina Hiseq 2500 (Novogene, Tianjin, China) platform with pair-end (2 × 300 bp) library. About 6.43 Gb of raw reads with 18,967,988 paired-end reads were obtained from high-throughput sequencing. The raw data was filtered using Trimmomatic v.0.32 with default settings (Bolger et al. Citation2014). Then paired-end reads of clean data were assembled into circular contigs using GetOrganelle.py (Jin et al. Citation2018) with Scutellaria baicalensis (NC027262) as reference. Finally, the cpDNA was annotated by the Dual Organellar Genome Annotator (DOGMA; http://dogma.ccbb.utexas.edu/) (Wyman et al. Citation2004) and tRNAscan-SE (Lowe and Chan Citation2016) with manual adjustment using Geneious v. 7.1.3 (Kearse et al. Citation2012).
The circular genome map was generated with OGDRAW v.1.3.1 (Greiner et al. Citation2019). Then the annotated chloroplast genome was submitted to the GenBank under the accession number MT012413. The total length of the chloroplast genome was 151,989 bp, with 37.8% overall GC content. With typical quadripartite structure, a pair of IRs (inverted repeats) of 25,579 bp was separated by a small single copy (SSC) region of 17,642 bp and a large single copy (LSC) region of 83,189 bp. The cp genome contained 113 genes, including 80 protein coding genes, 29 tRNA genes, and 4 rRNA genes.
To investigate its taxonomic status, a total of 24 cp genome sequences of Labiatae species were downloaded from the NCBI database used for phylogenetic analysis. After using MAFFT V.7.149 for aligning (Katoh and Standley Citation2013), a neighbor-joining (NJ) tree was constructed in MEGA v.7.0.26 (Kumar et al. Citation2016) with 1000 bootstrap replicates and four Oleaceae species Nicotiana otophora (NC 032724), Solanum melongena (MF818319), Physalis peruviana (MH019242) and Capsicum chinense (NC 030543) were used as outgroups. The results showed that Clinopodium was closely related to Mentha (). Meanwhile, the phylogenetic relationship in Labiatae was consistent with previous studies and this will be useful data for developing markers for further studies.
Figure 1. Neighbor-joining (NJ) tree of 25 species within the family Labiatae based on the plastomes using four Oleaceae species as outgroups.
Disclosure statement
The authors are highly grateful to the published genome data in the public database. The authors declare no conflicts of interest and are responsible for the content.
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