Abstract
Styrax calvescens Perk., is a nice tree, valued for its beauty and fragrance. Here, we characterized the complete chloroplast (cp) genome of S. calvescens using next-generation sequencing. The circular complete cp genome of S. calvescens is 157,951 bp in length, containing a large single-copy (LSC) region of 87,566 bp and a small single-copy (SSC) region of 18,289 bp. It comprises of 133 genes, including 8 rRNA genes, 37 tRNAs genes, and 88 protein-coding genes. The GC content of S. calvescens cp genome is 36.95%. The phylogenetic analysis suggests that S. calvescens is a sister species to Styrax grandiflorus Griffith in Styracaceae.
Keywords: Styrax calvescens, phylogenomics, Styracaceae, chloroplast genome
Styrax calvescens Perk. (Styracaceae), a nice tree with abundant white fragrant flowers blooming in late spring, is a multipurpose economic arbor species integrating ornamental, oil, and ornamental values. The complete genome sequence of S. calvescens plays an important role in the protection, development, and utilization of its resources. However, to date, there is still no complete cp genome that was characterized for S. calvescens, even for the genera Styrax. Here, we characterized the complete cp genome sequence of S. calvescens (GeneBank accession number: MN560141) based on Illumina pair-end sequencing to provide a valuable complete cp genomic resource.
Total genomic DNA was isolated from fresh leaves of S. calvescens habitated in Fuxi (30.03938 N, 118.09422E, Alt. 494 m) in Huangshan, Anhui, China. The voucher specimen was deposited at the herbarium of Nanjing Forestry University (accession number NF2019468). 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 v9 and the clean reading was assembled into chloroplast 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. Based on the Neighbor Joining (NJ), the phylogenetic tree was deduced by MAFFT (Katoh and Standley 2013) and MEGA version 7 (Kumar et al. 2016).
The circular genome of S. calvescens was 157,951 bp in size and contained 2 inverted repeat (IRa and IRb) regions of 26,048 bp, which were separated by a large single copy (LSC) region of 87,566 bp, and a small single copy (SSC) region of 18,289 bp. A total of 133 genes are encoded, including 88 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, 7 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7, ycf2, and ycf15), 7 tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 4 rRNA genes (4.5S, 5S, 16S, and 23S) are totally duplicated. A total of 9 protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, rps16, and rpl2) contained one intron while the other 3 genes (clpP, ycf3, rps12) had 2 introns each. The overall GC content of S. calvescens genome is 36.95% and the corresponding values in LSC, SSC, and IR regions are 34.78, 30.28, and 42.92%, respectively.
The phylogenetic analysis was conducted based on 24 Styracaceae cp genomes and 3 taxa (Symplocaceae, Actinidiaceae, and Theaceae) as outgroups with sequenced cp genomes. We found that S. calvescens was clustered with other families of Ericales with 100% boot-strap values (Figure 1). In addition, S. calvescens was highly supported to be a sister species to Styrax grandiflorus in Styracaceae. Furthermore, this study will pave the way for future research to understand the genomic information of the chloroplasts of the Styracaceae and this chloroplast resource could be utilized on the phylogeny, DNA barcoding, and conservation genetics.
Figure 1.
Neighbor Joining tree showing the relationship among 24 representative species within the Styracaceae, based on whole chloroplast genome sequences, with 8 species from Symplocaceae, Theaceae, Actinidiaceae as outgroup. The bootstrap support values shown at the branches.
Funding Statement
This research was supported by the Biodiversity Investigation, Observation and Assessment Program of Ministry of Ecology and Environment of China [2019001]; 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 [PAPD20181019].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability (Article). Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kumar S, Stecher G, Tamura K. 2016. Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Liu C, Shi LC, Zhu YJ, Chen HM, Zhang JH, Lin XH, Guan XJ. 2012. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics. 13(1):715. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lohse M, Drechsel O, Kahlau S, Bock R. 2013. Organellar Genome DRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41(W1):W575–W581. [DOI] [PMC free article] [PubMed] [Google Scholar]