The complete chloroplast genome of Isodon rubescens, a traditional Chinese herb

Abstract

Isodon rubescens (Hemsley) H. Hara is a kind of traditional medical herb which can be used for cancer treatment. In this study, the complete chloroplast genome sequence of I. rubescens was assembled. Its complete circular chloroplast DNA length was 152,761 bp. The genome was made up of a large single-copy region of 83,655 bp, a small single-copy region of 17,660 bp, and a pair of inverted repeat regions of 25,723 bp. The genome totally encoded 129 genes, containing 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that I. rubescens had a close relationship with basil (Ocimum basilicum).

Keywords:

• Isodon rubescens
• chloroplast genome
• phylogenetic tree

Isodon rubescens (Hemsley) H. Hara, also known as Rabdosia rubescens, is one of the important medical herbs in the Ocimeae tribe of Lamiaceae family (Neelamkavil and Thoppil 2017). Current phytochemical study had isolated several diterpenoids from I. rubescens, which showed positive functions to treat various diseases (Zhang et al. 2017). Oridonin as one of the identified diterpenoids was possible for the treatment of cancer, autoimmune, and inflammatory diseases through the inhibition of NF-κB (Leung et al. 2005). The key enzymes involved in terpenoid biosynthesis in I. rubescens were predicated through transcriptome analysis (Su et al. 2016). Lamiaceae is one of the largest family with more than 7000 species, which are classified into 12 primary clades (Li et al. 2016). The complete chloroplast genome sequences of I. rubescens can provide more useful information for phylogeny analysis and taxonomy.

The plant sample of I. rubescens was cultivated in the herb nursery of Xianyang (108.69E, 34.35 N), Shaanxi Province, China. The voucher specimen was deposited in the Herbarium of the Microbiology Institute of Shaanxi, Microbiology Institute of Shaanxi, China (zw2020003). The DNA from fresh leaves was extracted by the CTAB method (Porebski et al. 1997). The DNA insert fragments about 400 bp in length were used for library construction. Based on the Illumina Novaseq Platform at Personal Biotechnology Co. Ltd (Shanghai, China) and 2 × 150 bp pair-end sequencing mode, total 1.7 Gbp of sequencing data was generated (NCBI accession number: SRR13002570). The cleaned reads were assembled to form contig and scaffold via software of A5-MiSeq (v 20150522, Coil et al. 2015) and SPAdes (v 3.9.0, Bankevich et al. 2012). The locations of assembled contig sequences were determined using MUMmer (v 3.1, Kurtz et al. 2004) by Mentha × piperita as the reference genome (NCBI accession number: NC_047475.1). The assembled result was corrected via pilon (v1.18, Walker et al. 2014). The final chloroplast genome was annotated by CPGAVAS2 (Shi et al. 2019).

Using the next generation sequencing technology, we assembled a circular complete chloroplast genome of I. rubescens. The genome sequence and all gene annotations were submitted to the NCBI database with an accession number of MW018469. The complete chloroplast genome sequence was 152,761 bp in length. The genome was consisted of a large single-copy region (LSC, 83,655 bp), a small single-copy region (SSC, 17,660 bp), and two inverted repeat regions (IR, 25,723 bp). The whole genome encoded 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes.

To determine the evolutionary relationship between I. rubescens and other Lamiaceae species, a maximum-likelihood phylogenetic tree based on total 21 complete chloroplast sequences from Lamiaceae family was constructed (Figure 1). The species of Teucrium mascatense and Ajuga reptans from Ajugoideae subfamily were used as the outgroups. The GTRGAMMA + F+R3 model was chosen according to BIC and 1000 bootstrap replicates were used. All genome sequences were retrieved from the GenBank database. These sequences were aligned using MAFFT (v 7.407, Katoh and Standley 2013). Then, trimAl (v 1.4.1, Capella-Gutiérrez et al. 2009) was applied to remove poorly-aligned and divergent regions with algorithm automated1. The remaining sequences were used to infer the phylogenetic position using IQtree (v 1.6.12, Nguyen et al. 2015) under parameters ‘-nt AUTO -m MFP -bb 1000 –bnni’. The result showed that I. rubescens had a close relationship with basil (Ocimum basilicum).

Figure 1. Phylogenetic analysis of 21 complete chloroplast genomes from Lamiaceae family. The bootstrap support values are marked at the nodes.

Disclosure statement

No potential conflict of interest was reported by the author(s).

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/ under the accession no. MW018469. The associated BioProject, Bio-Sample, and SRA numbers are PRJNA674459, SAMN16657551, and SRR13002570 respectively.

Additional information

Funding

This research was supported by the Science and Research special Project of Education Department of Shaanxi Provincial Project [20JK0864], the Doctoral Scientific Research Foundation of Xi’an International University [XAIU2019014], and the Key Research and Development Program of Shaanxi Province [2020NY-197].