Complete chloroplast genome of medicinal plant Sabia parviflora Wall. ex Roxb. (Sabiaceae)

Abstract

Sabia parviflora Wall. ex Roxb., an evergreen climbing woody vine, is a Chinese herbal medicine commonly used by ethnic minorities in some areas of China. In this study, the chloroplast genome of S. parviflora was sequenced for the first time. Its genome is 162,054 bp in length with 38.6% of GC content. The genome consists of a large single copy (LSC) region of 90,001 bp, a small single copy (SSC) region of 18,887 bp, and two inverted repeat (IRa and IRb) regions of 26,583 bp each. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was conducted by nine species from order Proteales, which demonstrated a close relationship between the family Sabiaceae and Nelumbonaceae.

Keywords:

• Sabia parviflora
• Sabiaceae
• chloroplast genome
• medicinal plant

Sabia parviflora is an evergreen climbing woody vine of the genus Sabia (family Sabiaceae). It is native to Yunnan, Guizhou, and Guangxi province of China and is also distributed in India, Myanmar, Thailand, and other countries (ECFC 1988; Guo and Anthony 2007). As a traditional Chinese herbal medicine, S. parviflora is widely used to treat jaundice hepatitis, rheumatic arthritis, traumatic injury, and other diseases in some minority areas (Luo and Sun 2013). After recent years of research, it has been found that S. parviflora mainly contains terpenoids, alkaloids, flavonoids, etc., which have the effects of liver protection, antivirus, anti-rheumatic arthritis, anti-oxidation, and so on (Sun et al. 2019; Chen et al. 2020). At present, part of Chinese patent drugs and green tea have been developed with S. parviflora as raw material. However, as the most medicinally and economically valuable species in genus Sabia, the complete chloroplast genome of S. parviflora has not been reported, which restricted the taxonomic identification, phylogenetic analysis, and other studies of this genus. Therefore, this study sequenced the chloroplast genome of S. parviflora and the phylogenetic analysis was performed with species of Proteales.

Fresh leaves of S. parviflora were collected from Zhenning county, Guizhou province, China (E 105°36′24″, N 25°40′55″). Total DNA was extracted from those leaves using E.Z.N.A® Plant DNA Kit (OMEGA Bio-tek, Winooski, VT) according to the manufacturer’s instruction. The specimen and DNA sample were deposited in Herbarium of Guizhou University of Traditional Chinese Medicine (http://www.gzy.edu.cn/, Qingwen Sun, [email protected]) under the voucher number SABIA0728-07. The genome sequencing was conducted on the Illumina NovaSeq Sequencing System to generate paired-end 2*150 bp reads. Total about 5.43 Gb raw data were obtained. Trimmomatic (Bolger et al. 2014) was used to filter the raw data. NOVOPlasty (Dierckxsens et al. 2017) and CpGAVAS2 (Shi et al. 2019) were used to assemble and annotate the chloroplast genome, respectively, with the S. yunnanensis chloroplast genome sequences (NC_029431.1) as reference. The annotated genome sequence was submitted to the GenBank (Accession number: MW566751).

The chloroplast genome of S. parviflora is a double-stranded DNA molecule with a length of 162,054 bp. It presents a typical quadripartite structure, consisting of a large single copy (LSC) region, a small single copy (SSC) region, and two inverted repeat (IRa and IRb) regions. Its LSC and SSC regions are 90,001 and 18,887 bp, respectively, alternated by a pair of IR regions of 26,583 bp each. The overall GC content of this species is approximately 38.6% (LSC, 37.1%; SSC, 33.4%; IRs, 43.2%). A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among these genes, six protein-coding genes (rps12, rps7, rpl23, rpl2, ndhB, and ycf2), seven tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and all rRNA genes (rrn16, rrn23, rrn4.5, and rrn5) including two repeating units. Furthermore, there are 19 genes contain one intron, including 11 protein-coding genes (atpF, ndhA, ndhB × 2, petB, petD, rpl16, rpl2 × 2, rpoC1, and rps16) and 8 tRNA genes (trnA-UGC × 2, trnG-UCC, trnI-GAU × 2, trnK-UUU, trnL-UAA, and trnV-UAC). A total of four genes contain two introns (rps12×2, clpP, and ycf3). In addition, two genes (ycf1 and rps19) were annotated as pseudogenes.

The whole chloroplast genomes of nine species in four families of Proteales were used for phylogenetic analysis. After sequence alignment by MAFFT (Katoh and Standley 2013), MEGA X (Kumar et al. 2018) was used to perform maximum likelihood (ML) tree with the Tamura Nei model. The bootstrap method was used to test the reliability of phylogeny with 1000 replicates. Two species from Sabia showed a cognate relationship, and the family Sabiaceae have a closer relationship with family Nelumbonaceae than that of Platanaceae and Proteaceae (Figure 1). These relationships are congruent with previous report (Sun et al. 2016).

Figure 1. Phylogenetic relationships of nine Proteales species constructed from the complete chloroplast genome sequences using maximum likelihood (ML).

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] (https://www.ncbi.nlm.nih.gov/) under the accession no. MW566751. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA727714, SRR14455320, and SAMN19030660 respectively.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [Grant No. 81560707], First class discipline construction project in Guizhou Province [Grant No. GNYL [2017]008], Project of Engineering Research Center of Guizhou University [Grant No. KY [2017]018], and Excellent young scientific and Technological Talents Project of Guizhou Province [Grant No. [2019]5658].