The complete chloroplast genome sequence of Styrax chinensis Hu et S.Y. Liang (Styracaceae)

Abstract

Styrax chinensis Hu et S.Y. Liang, is one of the few evergreen species of Styracaceae with fragrant flowers. Here, we characterized the complete chloroplast (cp) genome of S. chinensis using next-generation sequencing. The circular complete cp genome of S. chinensis is 158,502 bp in length, containing a large single-copy (LSC) region of 87,817 bp, and a small single-copy (SSC) region of 18,001 bp. It comprises 132 genes, including 8 rRNA genes, 37 tRNAs genes, and 87 protein-coding genes. The GC content of S. chinensis cp genome is 36.93%. The phylogenetic analysis suggests that S. chinensis is a sister species to Styrax suberifolius in Styracaceae.

Keywords:

• Styrax chinensis
• phylogenomics
• Styracaceae
• complete chloroplast genome

Styrax chinensis Hu et S.Y. Liang is a rare evergreen member of Styrax, trees, 5–20 m tall. Trunk to 34 cm d.b.h, mainly distributed in tropical and subtropical lowland areas (Huang and Grimes 2003). It possesses high values for medicinal, ornamental, and timber (Liang 1981). Due to no complete cp genome was characterized for S. chinensis. We characterized the complete cp genome sequence of S. chinensis (GeneBank accession number: MT648752) based on Illumina pair-end sequencing to provide a valuable complete cp genomic resource.

Total genomic DNA was isolated from fresh leaves of S. chinensis grown in Qingxiu mountain (N 22.4711, E 108.2240), Nanning, Guangxi, China. The voucher specimen was deposited at the herbarium of Nanjing Forestry University (accession number NF2020091). The whole genome sequencing was carried out on Illumina Hiseq platform by Nanjing Genepioneer Biotechnology Inc. (Nanjing, China). The original reading was filtered by CLC Genomics Workbench version 9, and the clean reading was assembled into chloroplast (cp) genome with SPAdes (Bankevich et al. 2012). Finally, CpGAVAS (Liu et al. 2012) was used to annotate the gene structure and OGDRAW (Lohse et al. 2013) was used to generate the physical map.

The circular genome of S. chinensis was 158,502 bp in size and contained two inverted repeat (IRa and IRb) regions of 26,342 bp, which were separated by a large single-copy (LSC) region of 87,817 bp, and a small single-copy (SSC) region of 18,001 bp. A total of 134 genes are encoded, including 87 protein-coding genes (81 PCG species), 37 tRNAs gene (30 tRNA species), and 8 rRNA genes (4 rRNA species). Most of the genes occurred in a single copy; however, seven protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7, ycf2, and ycf15), seven tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and four RNA genes (4.5S, 5S, 16S, and 23S) are totally duplicated. A total of nine protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, rps16, and rpl2) contained 1 intron while the other three genes (clpP, ycf3, rps12) had 2 introns each. The overall GC content of S. chinensis genome is 36.93%, and the corresponding values in LSC, SSC, and IR regions are 34.77, 30.34, and 42.78%, respectively.

In order to show the position of S. chinensis in Styracaceae, we collected 36 Styracaceae cp genomes and three taxa (Symplocaceae, Actinidiaceae, and Clethraceae) as outgroups with sequenced cp genomes. Sequences were aligned with MAFFT (Rozewicki et al. 2019). A phylogenetic tree was constructed based on the maximum likelihood (ML) with MEGA version 7 (Kumar et al. 2016). The results show that S. chinensis was clustered with other families of Styracaceae with 100% boot-strap values (Figure 1). In addition, S. chinensis was highly supported to be a sister species to Styrax suberifolius in Styracaceae.

Figure 1. Maximum likelihood tree showing the relationship among Styrax chinensis and representative species within Styracaceae, based on whole chloroplast genome sequences, with 3 taxa from Ericales as outgroup. The bootstrap supports the values shown at the branches.

Disclosure statement

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

Data availability statement

The data is accessible from: https://pan.baidu.com/s/1GrqhmarC1h6WID-WPLwXdQ (password：rxqn).

Additional information

Funding

This research work was supported by: The Biodiversity Investigation, Observation and Assessment Program of Ministry of Ecology and Environment of China [20191226]; The Special Fiscal Funds for Repair and Purchase in National Public Institutions [2010002002]; Jiangsu Forestry Science and Technology Innovation and Extension Program [No. LYKJ[2018]13]; The Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).