Abstract
Styrax agrestis (Lour.) G. Don, is a deciduous species of Styracaceae with beautiful shape, drooping flowers, and blooming like snow. Here, we characterized the complete chloroplast (cp) genome of S. agrestis using next generation sequencing. The circular complete cp genome of S. agrestis is 157,893 bp in length, containing a large single-copy (LSC) region of 87,512 bp, and a small single-copy (SSC) region of 18,285 bp. It comprises 136 genes, including eight rRNA genes, 37 tRNAs genes, 90 protein-coding genes, and one pseudo gene. The GC content of S. agrestis cp genome is 36.96%. The phylogenetic analysis suggests that S. agrestis is a sister species to Styrax faberi in Styracaceae.
Keywords: Styrax agrestis, phylogenomics, Styracaceae, complete chloroplast genome
Styrax agrestis (Lour.) G. Don is mainly distributed in tropical and subtropical lowland areas in Southeast Asia. Currently, S. agrestis possesses high value for ornamental, timber, and medicinal purposes (Huang and Grimes 2003). So far, there is still no complete cp genome characterized for S. agrestis. Here, we characterized the complete cp genome sequence of S. agrestis (GenBank accession number: MT644192) based on Illumina pair-end sequencing to provide a valuable complete cp genomic resource.
Total genomic DNA was isolated from fresh leaves of S. agrestis grown in Jianfengling, Ledong County (N 18.4210, E 108.5055), Hainan, China. The voucher specimen was deposited at the herbarium of Nanjing Forestry University (accession number: NF2020090). The whole genome sequencing was carried out on Illumina Hiseq platform by Nanjing Genepioneer Biotechnology Inc. (Nanjing, China). The original reads were filtered by CLC Genomics Workbench v9, 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. Based on the maximum likelihood (ML), the phylogenetic tree was deduced by MAFFT (Rozewicki et al. 2019) and MEGA version 7 (Kumar et al. 2016).
The circular genome of S. agrestis was 157,893 bp in size and contained two inverted repeat (IRa and IRb) regions of 26,048 bp, which were separated by a large single-copy (LSC) region of 87,512 bp, and a small single-copy (SSC) region of 18,285 bp. A total of 136 genes are encoded, including 90 protein-coding genes (82 CDS species), 37 tRNAs gene (30 tRNA species), eight rRNA genes (four rRNA species), and one pseudo gene. Most of genes occurred in a single copy; however, eight protein-coding genes (ndhB, orf42, 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 rRNA 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 one intron while the other three genes (clpP, ycf3, rps12) had two intron each. The rest of the 70 protein-coding genes are psaA, psaB, psaC, psaI, psaJ, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK, petA, petG, petL, petN, atpA, atpB, atpE, atpH, atpI, rbcL, rpl14, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36, rps11, rps14, rps15, rps18, rps19, rps2, rps3, rps4, rps7, rps8, rpoA, rpoB, rpoC2, matK, cemA, accD, ccsA, infA, lhbA, orf188, orf42, ycf1, ycf15, ycf2, and ycf4. The overall GC content of S. agrestis genome is 36.96%, and the corresponding values in LSC, SSC, and IR regions are 34.81%, 30.29%, and 42.92%, respectively.
The phylogenetic analysis was conducted based on 35 Styracaceae cp genomes and three taxa (Symplocaceae, Ebenaceae, and Clethraceae) as outgroups with sequenced cp genomes. We found that S. agrestis was clustered with other families of Styracaceae with 100% bootstrap values (Figure 1). In addition, S. agrestis was highly supported to be a sister species to Styrax faberi in Styracaceae.
Figure 1.
Maximum-likelihood tree showing the relationship among Styrax agrestis and representative species within Styracaceae, based on whole chloroplast genome sequences, with three taxa from Ericales as outgroup. The bootstrap supports the values shown on the branches.
Funding Statement
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 [LYKJ[2018]13]; The Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).
Disclosure statement
No potential conflict of interest was reported by the authors.
Data availability statement
The raw sequence data are accessible from: https://pan.baidu.com/s/15eih-q4yDMD4sjosDLo7yA (password: acvm) the GenBank accession number: MT644192.
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]
- Huang S-M, Grimes JW.. 2003. Styracaceae. In: Wu Z-Y, Raven PH, Hong D-Y, editors. Flora of China, vol. 15 (Styracaceae). Beijing/St. Louis: Science Press/Missouri Botanic Garden Press; p. 258. [Google Scholar]
- Kumar S, Stecher G, Tamura K.. 2016. MEGA7: 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. 13:715. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lohse M, Drechsel O, Kahlau S, Bock R.. 2013. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41(Web Server issue):W575–W581. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rozewicki J, Li S, Amada KM, Standley DM, Katoh K.. 2019. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res. 47(W1):W5–W10. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The raw sequence data are accessible from: https://pan.baidu.com/s/15eih-q4yDMD4sjosDLo7yA (password: acvm) the GenBank accession number: MT644192.