Characterization of the complete chloroplast genome of Incarvillea arguta (Bignoniaceae)

Abstract

IIncarvillea arguta belongs to the family Bignoniaceae, is an economically and medicinally important plant. The complete chloroplast genome of I. arguta is 159,135 bp in size, including a large single copy (LSC) region of 87.192 bp, a small single copy (SSC) region of 19,023 bp and a pair of inverted repeats (IRs) of 26,460 bp. The genome contains 108 genes, including 72 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. The GC content in chloroplast genome, LSC region, SSC region, and IR region were 39.5%, 37.9%, 34.7%, and 43.7%, respectively. The evolutionary analysis suggested that I. arguta is related to Tecomaria capensis.

Keywords:

• Incarvillea arguta
• chloroplast genome
• phylogenetic relationship

Incarvillea arguta (Royle) Royle is an economically and medicinally important herb plant, which is widely distributed in the dry-hot valley regions in the Qinghai-Tibetan Plateau and Himalayas. Previous studies had mainly focused on the chemical constituents (Zhou et al. 2007), sesquiterpenoids configuration, and biological evaluation (Luo et al. 2004; Yan et al. 2012) of this species. In this study, we sequenced and assembled the complete chloroplast genome (cpDNA) of I. arguta, which has been deposited into the GenBank with the accession number MG763885.

Fresh leave materials of I. arguta were collected from Xiaojin county, Sichuan, China (N31.01°, E102.04°), and the plant materials and a voucher specimen (No. IAGTX2015067) were stored in Northwest University. Total genomic DNA was isolated using the improved CTAB method (Doyle and Doyle 1987), and sequenced with Illumina Hiseq 2500 (San Diego, CA, USA) platform. All raw reads were trimmed using the program NGSQCToolkit_v2.3.3 (Patel and Jain 2012). After dislodged the low-quality reads, the clean reads were assembled by MIRA v4.0.2 (Chevreux et al. 2004) and MITObim v1.8 (Hahn et al. 2013) using the chloroplast genome of Tanaecium tetragonolobum (NC_027955) as a reference.

The chloroplast complete genome of I. arguta is 159,135 bp in size, including a large single copy (LSC) region of 87.192 bp, a small single copy (SSC) region of 19,023 bp and a pair of inverted repeats (IRs) of 26,460 bp. The GC content in chloroplast genome, LSC region, SSC region and IR region were 39.5%, 37.9%, 34.7%, and 43.7%, respectively. The genome contains 108 genes, including 72 protein-coding genes, 32 tRNA genes, and 4 rRNA genes.

A total of 16 species were used to construct the phylogenetic tree among the most of Lamiales species with Verbenaceae, Lentibulariaceae, and Labiatae species as outgroups. Modeltest v3.7 (Posada and Crandall 1998) was used to determine the best-fitting model for the chloroplast genomes. Maximum likelihood analysis was performed using RAxML (Stamatakis 2014) with 1000 bootstrap replicates. The results showed that I. arguta is closely related to Tecomaria capensis (Figure 1). The complete chloroplast genome of I. arguta can be subsequently used for the phylogenetic reconstruction and comparative genomics analysis of Bignoniaceae.

Figure 1. Maximum likelihood (ML) tree of I. arguta based on the chloroplast complete genome sequence.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was co-supported by the National Natural Science Foundation of China [41461075] and the National Undergraduate Innovation and Entrepreneurship Training Program [201510740007].