Complete chloroplast genome sequence and phylogenetic analysis of Sinojackia sarcocarpa, an endemic plant in Southwest China

Abstract

Sinojackia sarcocarpa is an endangered plant endemic to China. Here, the complete chloroplast genome of S. sarcocarpa was sequenced and characterized. The total genome size is 158,737 bp, with a typical quadripartite structure including a pair of inverted repeat regions (IRs, 26,090 bp) separated by a large single copy (LSC, 88,002 bp) region and a small single copy (SSC, 18,555 bp) region. The genome contains 137 genes, including 90 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis revealed that S. sarcocarpa is closely related to Sinojackia xylocarpa and Sinojackia rehderiana, but forms an independent evolutionary branch.

Keywords:

• Sinojackia sarcocarpa
• chloroplast genome
• styracaceae
• illumina sequencing

Sinojackia sarcocarpa is a Styracaceae plant endemic to Sichuan province, China (Luo 1992). Sinojackia sarcocarpa has good ornamental value and can be used as a garden tree species. In addition, it contains effective anticancer compounds and can be used as an important plant source for the extraction of drug active substances (Wang et al. 2011). However, the number of existing wild individuals is very small, S. sarcocarpa is, therefore, under state protection (category II) in China. A good knowledge of its phylogeny and taxonomy is necessary for the protection and utilization of S. sarcocarpa. Molecular systematics has become an important method of taxonomic research. In the past, system evolution was usually inferred by selecting individual or several genes, however, single-gene data lacks sufficient genetic information when compared to the multi-gene data (Thorne and Kishino 2002). The chloroplast genome structure is conservative, rarely recombinant, and mutated, and is uniparental inheritance in most cases, so it is of great practical value to study the evolution of plant system (He et al. 2019). However, at present, no complete chloroplast genome sequence of S. sarcocarpa is available in the NCBI GenBank. This work is the first to report on the chloroplast genome sequence of S. sarcocarpa, which can better understand the genetic background of S. sarcocarpa and contribute to the conservation of the species.

The samples of S. sarcocarpa were collected from botanical garden in Leshan, Sichuan Province, China and the specimens were stored in the herbarium of Leshan normal university. Total genomic DNA was extracted from 50 mg fresh leaves using SDS method. The complete chloroplast genome of S. sarcocarpa was sequenced by Illumina HiSeq Xten platform, the Illumina raw sequence reads were edited by the NGS QC tool Kit v2.3.3, the percentage of cut-off values for read length and phred quality score were 80 and 30, respectively (Patel and Jain 2012). High-quality readings were assembled by SPAdes3.9.0 software, and the K-mer set values were selected as 93, 105, 117, 121 (Bankevich et al. 2012). Annotations were performed with the plann software (Huang and Cronk 2015). The complete chloroplast genome of S. sarcocarpa (GenBank accession number MK351986) is 158,737 bp in length, which has a GC content of 37.24%, including a large single-copy area (LSC, 88,002 bp) and a small single-copy area (SSC, 18,555 bp), as well as two reverse repetition zones (IRs) of 26,090 bp. The complete chloroplast genome encodes 137 genes, including 90 protein-coding genes, 8 ribosomal RNA genes, and 38 transfer RNA genes, 15 genes contain an intron, 2 genes contain two introns, and 1 rps12 gene has trans splicing.

To ascertain the phylogenetic evolution of S. sarcocarpa, the fasta format file containing all the chloroplast genome sequences of 24 plants was treated by MAFFT 7.037 software and then aligned in automatic mode (Katoh and Standley 2013). The neighbour-joining (NJ) phylogenetic tree was constructed by MEGA 6.0 software (Tamura et al. 2013), the parameter settings were as follows: the stability of branches was evaluated with 1,000 bootstrap replications, nucleotide substitution model was computed using the p-distance method, the substitution included a variety of transitions and transversions, and the gaps/missing data treatments were set to complete deletion. The results of phylogenetic analysis show that S. sarcocarpa forms a separate branch when compared with other plants in this study, which is more closely related to two other Sinojackia species (Figure 1). The complete plastome sequence of S. sarcocarpa provides an important data set for the conservation genetics of this species.

Figure 1. The NJ phylogeny constructed from 24 complete plastome sequences using MEGA6.0 software. Note: Numbers near each node represent the percentage of support when the nodes occurred among 1000 bootstraps.

Disclosure statement

The authors confirm this article content has no conflict of interest and all the authors are responsible for the content of this article.

Additional information

Funding

This work was supported by Leshan Normal University under Grant JG2018-1-ZF-21.