The complete mitochondrial genome sequence of Schisandra chinensis (Austrobaileyales: Schisandraceae)

Abstract

Chinese magnolia vine (Schisandra chinensis) is an economically important oriental medicinal plant that belongs to the Schisandraceae family. The complete mitochondrial genome sequence of S. chinensis was 946,141 bp in length. A total of 45 genes was annotated, including 30 protein-coding genes, 12 tRNA genes, and 3 rRNA genes. A phylogenetic tree based on the mitochondrial genome demonstrated that S. chinensis was most closely related to Schisandra sphenanthera of the Schisandraceae family.

Main

Chinese magnolia vine (Schisandra chinensis), a medicinal plant belonging to the Schisandraceae family, grows in China, Japan, Korea, and Russia and is well-known in both traditional and modern Chinese medicine (Chun et al. 2014). Schisandra chinensis has been reported to have several medicinal effects, including for gastrointestinal issues, respiratory failure, insomnia, body fatigue, delaying the aging process, excessive sweating, and cardiovascular protective activity (Szopa et al. 2017).

A sample was obtained from the Jeollabukdo Medicinal Resource Research Institute (voucher number: JA2018-117, geographic coordinate: N 35°46′10″, E 127°22′40″) in Jinan, Korea. Whole genome sequencing was performed using the Illumina Miseq platform (Illumina, CA, USA), the Nanopore GridION platform (Oxford Nanopore Technologies, Oxford Park, UK), and the PacBio RSII platform (Pacific Biosciences, Menlo Park, CA, USA). A total of 7.6 Gb of raw read bases were generated and low-quality bases (<Q20) were trimmed using the NGS QC Toolkit (Patel and Jain 2012). First, initial contigs were generated using a hybrid assembly of Illumina Miseq data and Nanopore sequencing data using the SPAdes assembler (Bankevich et al. 2012). Second, selected contigs were subjected to gap-filling procedures and error-corrected using the CLC Assembly Cell package (QIAGEN Bioinformatics, CA, USA). Finally, genes were annotated using Mitofy and BLAST searches (Alverson et al. 2010).

The complete mitochondrial genome of S. chinensis was a circular form 946,141 bp in length. The genome harbored 45 annotated genes, including 30 protein-coding genes, 12 tRNA genes, and 3 rRNA genes. The complete mitochondrion of S. chinensis (Accession no. MK860624) was registered to NCBI GenBank.

Genome alignments were performed using MAFFT (Yamada et al. 2016), and a phylogenetic tree was constructed using MEGA 7.0 (Kumar et al. 2016). The phylogeny was generated using 11 reported species, and phylogenetic relationships were analyzed using five common protein-coding genes (nad3, nad6, nad9, rpl5, and rps12), which exists completely within the initiation and stop codon.

Our phylogeny analysis indicated that S. chinensis is most closely related to Schisandra sphenanthera of the Schisandraceae family (Figure 1). Clinically, S. chinensis and S. sphenanthera have different pharmacological effects, although there are reports that these two species have common main components (Lu and Chen 2009). This finding is expected to contribute to the development of molecular markers for herbal drugs in the Schisandraceae family.

Figure 1.

Phylogeny of S. chinensis and 11 related species based on their mitochondrial genome sequences. The phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicates based on five common protein-coding genes from the mitochondrial genomes of 12 species.

Geolocation

The genomic DNA sample used for sequencing was obtained from the Jeollabukdo Medicinal Resource Research Institute (geographic coordinate: N 35°46′10″, E 127°22′40″).

Disclosure statement

The authors report no conflicts of interest.