The first complete chloroplast genome sequence of the medicinal plant Bupleurum marginatum (Apiaceae)

Abstract

Bupleurum marginatum is a medicinal plant commonly used in China. In this study, we sequenced the complete chloroplast (cp) genome sequence of B. marginatum to investigate its phylogenetic relationship in the family Apiaceae. The chloroplast genome of B. marginatum was 154,991 bp in length with 37.8% overall GC content, including a large single-copy (LSC) region of 84,904 bp, a small single-copy (SSC) region of 17,479 bp and a pair of inverted repeats (IRs) of 26,304 bp. The cp genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated B. marginatum was closely related to B. latissimum.

Keywords:

• Bupleurum marginatum
• chloroplast
• Illumina sequencing
• phylogeny

Bupleurum is a large genera of the family Apiaceae, which includes 150 species in the world (Burtt 1991). Most of them are mainly distributed in Europe, North Africa, Macaronesia (Canary Islands and Madeira), Asia and North America (Neves and Watson 2004). There are 42 species in China (She and Watson 2005). The roots of some species in this genus, namely Radix Bupleuri, have been widely used in traditional Chinese medicine for thousands of years (Jiangsu New Medical College 1977). In Chinese pharmacopeia (National Pharmacopoeia Committee 2015), the species Bupleurum chinense and Bupleurum scorzonerifolium, were the original species of the Radix Bupleuri and recorded in that. But in some region of China, the roots of the species Bupleurum marginatum are commonly used as the Radix Bupleuri in local medicine for treatment of coughs, fevers, and influenza (Jiangsu New Medical College 1977). However, to date for such medicinal plant, many studies have mainly focused on describing its chemical compositions and pharmacological studies (Guan et al. 2005; Yao et al. 2019), with little involvement in its genomic analysis, so that no comprehensive genomic resource is conducted for it. Here, we report the chloroplast genome sequence of B. marginatum and find its internal relationships within the family Apiaceae.

Fresh and clean leave materials of B. marginatum were collected from Lixian county, Sichuan, China (N31°40′27.49″, E102°45′44.28″), and the plant materials and a voucher specimen (No. DXD05) were stored in Guangzhou University of traditional Chinese Medicine. Chloroplast DNA (cpDNA) extracted following the directions of DNeasy Plant Mini Kit (Qiagen, CA, USA). The whole genome sequencing was conducted on the Illumina HiSeq X Ten Sequencing System in Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). The raw data were filtered using Trimmomatic v.0.32 with default settings (Bolger et al. 2014). Then paired-end reads of clean data were assembled into circular contigs using SOAPdenovo2 (Luo et al. 2012) with Bupleurum latissimum (No. NC_033346) as reference. Finally, the cpDNA was annotated by the Dual Organellar Genome Annotator (DOGMA; http://dogma.ccbb.utexas.edu/) (Wyman et al. 2004) and tRNAscan-SE (Lowe and Chan 2016) with manual adjustment using Geneious v. 9.1.2 (Kearse et al. 2012).

The circular genome map was generated with OGDRAW v.1.3.1 (Greiner et al. 2019). Then, the annotated chloroplast genome was submitted to the GenBank under the accession number MN968501. The total length of the chloroplast genome was 154,991 bp, with 37.8% overall GC content. With typical quadripartite structure, a pair of IRs (inverted repeats) of 26,304 bp was separated by a small single-copy (SSC) region of 17,479 bp and a large single-copy (LSC) region of 84,904 bp. The cp genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Of these, 17 genes (rpl2, rpl23, trnI-CAU, ycf2, trnL-CAA, ndhB, rps7, rps12, trnV-GAC, rrn16, trnI-GAU, trnA-UGC, rrn23, rrn4.5, rrn5, trnR-ACG, trnN-GUU) were duplicated in the inverted repeat regions, 10 genes (rps16, atpF, rpoC1, petB, petD, rpl16, rpl2, ndhB, rps12, ndhA), and 6 tRNA genes (trnK-UUU, trnG-GCC, trnL-UAA, trnV-UAC, trnI-GAU, trnA-UGC) contain one intron, while two genes (ycf3 and clpP) have two introns.

To investigate its taxonomic status, a total of 33 cp genome sequences of Apiaceae species were downloaded from the NCBI database used for phylogenetic analysis. After using MAFFT V.7.149 for aligning (Katoh and Standley 2013), a neighbor-joining (NJ) tree was constructed in MEGA v.7.0.26 (Kumar et al. 2016) with 1000 bootstrap replicates and three Araliaceae species (Panax notoginseng: NC_026447, Panax ginseng: AY582139, and Panax quinquefolius: KT028714) were used as outgroups. The results showed that Bupleurum marginatum was closely related to Bupleurum latissimum and the genus Bletilla was sister to Pleurospermum or Chamaesium (Figure 1). Meanwhile, the phylogenetic relationship in Apiaceae was consistent with previous studies and this will be useful data for developing markers for further studies.

Figure 1. Neighbor-joining (NJ) tree of 34 species within the family Apiaceae based on the plastomes using three Araliaceae species as outgroups.

Disclosure statement

The authors are highly grateful to the published genome data in the public database. No potential conflict of interest was reported by the author(s).