The complete chloroplast genome of the endangered species Oyama sinensis (Magnoliaceae)

Abstract

Oyama sinensis is a large deciduous shrub endemic to Sichuan Province, China. Here, we assembled and characterized the complete chloroplast genome of O. sinensis using Illumina sequencing data. Our assembled chloroplast genome is 160,127 base pairs (bp) in length, containing a large single-copy (LSC) region of 88,206 bp, a small single-copy (SSC) region of 18,783 bp, and two inverted repeat (IR) regions of 26,569 bp. The chloroplast genome possesses total 131 genes, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. In addition, phylogenetic analyses show that O. sinensis is closely related to Yulania liliiflora.

Keywords:

• Oyama sinensis
• chloroplast genome
• endangered species
• phylogeny

Oyama sinensis (Rehder & E. H. Wilson) N. H. Xia & C. Y. Wu (Magnoliaceae) is a large deciduous shrub known only from the mountain forests in Sichuan Province, China (Xia et al. 2008). This species has attracted horticultural interest due to the flowers, which are fragrant and showy—white, cup-shaped, 8–12 cm in diameter, with prominent crimson stamens. In addition, the bark of O. sinensis is used in traditional Chinese medicine. Currently, O. sinensis is significantly threatened by habitat loss and considered to be one of the plant species with extremely small populations in the wild (Pan et al. 2014). The species is listed as Vulnerable (VU) based on the IUCN Red List criteria (http://www.iucnredlist.org/), and under second-class national protection in China (http://www.forestry.gov.cn/yemian/minglu1.htm). To date, little is known about the population genetics of O. sinensis. Therefore, understanding the genomic characteristics of this endangered species is important for developing conservation strategies. Here, we assembled and characterized the complete chloroplast genome of O. sinensis using Illumina sequencing data.

We sampled a single individual of O. sinensis collected from Yingjing County, Sichuan (GPS coordinates: 29°39′40.7″N, 102°36′46.4″E). A voucher specimen (ZhangLS-20180608) was deposited in the Sichuan University Herbarium (SZ). The total genomic DNA was extracted from fresh leaves using a modified CTAB method (Doyle and Doyle 1987). The filtered reads were assembled by the program NOVOPlasty (Dierckxsens et al. 2017) for O. sinensis using the sequenced chloroplast genome of its close relative Manglietia insignis (Wallich) Blume (Zheng and Xu 2018) as the reference. Next, the assembled chloroplast genome was annotated using Geneious (Kearse et al. 2012), and the physical map was generated using OGDRAW (Lohse et al. 2013). The chloroplast genome together with gene annotations was submitted to GenBank under the accession number of MK176508. To further investigate its phylogenetic placement, a neighbour-joining tree (Saitou and Nei 1987) was constructed by including 13 additional Magnoliaceae species. Here, DNA sequences from these 14 chloroplast genomes were first aligned using MAFFT (Katoh and Standley 2013), and a phylogenetic tree was then constructed using MEGA7 (Kumar et al. 2016) with 1000 bootstrap replicates.

The chloroplast genome of O. sinensis is 160,127 base pairs (bp) in size, containing a large single-copy (LSC) region of 88,206 bp, a small single-copy (SSC) region of 18,783 bp, and two inverted repeat (IR) regions of 26,569 bp. The chloroplast genome possesses total 131 genes, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Most of these genes are in a single copy, however, four rRNA genes (4.5S, 5S, 16S, and 23S rRNA), seven protein-coding genes (ndhB, rpl2, rpl23, rps7, rps12, ycf2, and ycf15), and seven tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC) occur in double copies. The overall GC-content of the whole chloroplast genome is 39.2%, while the corresponding values of the LSC, SSC, and IR regions are 37.9%, 34.3%, and 43.2%, respectively. In addition, phylogenetic analyses show that O. sinensis is closely related to Yulania liliiflora with a 100% bootstrap support (Figure 1).

Figure 1. Phylogenetic relationships of Oyama sinensis based on complete chloroplast genome sequences. Bootstrap percentages and GenBank accession numbers are indicated for each branch and taxon, respectively.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Additional information

Funding

This work was supported by the National Key Research and Development Program of China under Grant 2017YFC0505203.