Characterization of the complete mitochondrial genome of shrubby sophora (Sophora flavescens Ait.)

Abstract

Sequencing the Sophora flavescens mitochondrial genome is important for elucidating the evolutionary characteristics of traditional Chinese medical plants. In this study, the complete mitochondrial (mt) genome of S. flavescens was sequenced through Illumina sequencing method, and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 494,369 bp S. flavescens mitochondrial genome has a total of 78 genes, including 53 protein-coding genes, three rRNA genes, and 23 tRNA genes. The overall GC content of this mitogenome is 44.9%. By phylogenetic analysis using maximum likelihood method, S. flavescens showed the closest relationship with Vigna radiata in the clade of Papilionoideae.

Keywords:

• Sophora flavescens
• mitochondrial genome
• Illumina sequencing
• phylogenetic analysis

The shrubby sophora (Sophora flavescens) is a species of plant in the genus Sophora, which belongs to the Fabaceae family. It is a traditional Chinese medicine that has been used for anti-tumor, viral hepatitis, enteritis, viral myocarditis, arrhythmia, and skin diseases. Here, we assembled and analyzed the mitochondrial genome of S. flavescens based on the next-generation sequencing method.

Plant materials of S. flavescens Ait. sequenced in this study were acquired from medical plants garden in Guiyang University of Traditional Chinese Medicine (26°57'N, 106°72'W). Both the materials and its total genomic DNA and were stored in the Key Laboratory of Miao Medicine, Guiyang University of Traditional Chinese Medicine. Sequencing was done on an Illumina HiSeq2500 platform. The clean reads were assembled using SPAdes 3.11.1 (Bankevich et al. 2012) with default settings.

We used other mitochondrial genomes from higher plants as seeds to collect the mitochondrial contigs as much as possible. To fill the gap, Price (Ruby et al. 2013) and MITObim v1.8 (Hahn et al. 2013) were applied and Bandage (Wick et al. 2015) was used to construct the circular assembly path guided by these positions of long scaffolds. The complete sequence was primarily annotated using Plann (Huang and Quentin 2015) and Exonerate (Slater Guy St. C. and Birney Ewan 2005) combined with manual correction. All tRNAs were confirmed using the tRNAscan-SE search server (Lowe and Sean 1997). Other protein-coding genes were verified using BLAST search on the NCBI website, and manual correction for start and stop codons was conducted. This complete mitochondrial genome sequence was submitted to GenBank under the accession numbers of MH922916.

Mitochondrial genome of S. flavescens Ait. is a typical circular structure of 494,369 bp with a GC content of 44.9%. This mitochondrial genome contains a total of 78 genes, including 53 protein-coding genes, three rRNA genes (rrn5, rrn18, and rrn26), 17 complete native mitochondrial tRNA genes, and six chloroplast-derived tRNA genes.

Another 25 published complete mitochondrial sequences of Spermatophyta were downloaded from the NCBI database. Eight shared protein-coding genes were selected for phylogenetic analysis. These nucleotide sequences were separately aligned using PRANK (Löytynoja Ari and Nick Goldman 2010). After trimming using Gblocks (Dereeper et al. 2008), the independent alignments were subsequently concatenated. ModelFinder (Kalyaanamoorthy et al. 2017) was used to identify the most appropriate substitution model. Phylogenetic analyses of the concatenated sequences were performed using the maximum likelihood (ML) method implemented in IQ-TREE version 1.6.6 (Nguyen et al. 2014) according to the optimal substitution models under the rapid bootstrap algorithm (1000 replicates). To test support for the branch points of each gene trees, nonparametric branch support tests based on the Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-like aLRT) procedure were also performed in the same run. As shown in Figure 1, the phylogenetic positions of these 26 mt genomes were successfully resolved with full bootstrap supports across almost all nodes. S. flavescens Ait., belonging to the Sophoreae, exhibited the closest relationship with Vigna radiata in the clade of Papilionoideae.

Figure 1. Phylogenetic tree yielded by ML analysis of 26 higher plant mt genomes. ML consensus tree is shown with bootstrap supports indicated by numbers besides branches.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Guizhou TCM modernization project [No. 3029-3, 2014], Innovation Team Project from Education Department of Guizhou Province [No. 12, 2013], and Open Project from Guizhou Key Laboratory of Miao Medicine [No. 8, 2017].