Abstract
Camellia octopetala is a native oil tree species in the south of China and is also a unique natural Chinese woody edible oil species. In the study, the complete plastid genome was assembled and annotated, the genome full-length is 156,615 bp, contains a large single-copy (LSC) region with 86,273 bp, a small single-copy (SSC) region with 18,410 bp, two invert repeats (IR) regions with 25,966 bp. The plastid genome contains 135 genes, 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis shows C. octopetala sister to C. crapnelliana and embedded in Camellia.
Keywords: Camellia octopetala, plastid genome, phylogeny
Camellia octopetala belongs to Camellia genus which contains about 120 species all over the world (eFloras 2008). China is a Camellia hot spot which contains 97 species (76 endemic) and mainly distributed in Yunan Province, Guangxi Province, Guangdong Province, Sichuan Province of China. Camellia octopetala is an evergreen microphanerophyte which is mostly discovered in the understory of the forest with high air humidity, south of China. The species is an economic species which is known for its high oil content of its seeds, similar with the C. oleifera (Zhang et al. 2017). Here, we present the study which was assembled and characterized the plastid genome of C. octopelata as a resource for evolution and breeding research.
The plant sample of C. octopetala was collected from Fujian province, China (Youxi, Sanming: 118°15′32″E, 26°22′07″N) and dried into silica gel immediately. The voucher specimen is deposited at the Herbarium of College of Forestry, Fujian Agriculture and Forestry University (specimen code FJFC04028). DNA extraction from fresh leaf tissue and randomly interrupted using the Covaris ultrasonic breaker for library construction. The 350 bp library was prepared with a NEBNext® Ultra TM DNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA). Genome was sequenced by PE150 by Illumina Novaseq platform, approximately 10 GB data generated. Raw data quality trimmed by NGSQC with default parameters. Complete plastid genome of C. octopetala was assembled by SPAdes 3.9.0 (Bankevich et al. 2012) and MITObim v1.8 (Hahn et al. 2013) with default parameters. Assembled chloroplast genome annotation by DOGMA (Wyman et al., 2004) and CpGAVAS (Liu et al. 2012). The annotation result was drawn with OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013).
The complete plastid genome sequence of C. octopetala (GenBank accession MN095258) was 156,615 bp in length with a large single-copy (LSC) region of 86,273 bp, a small single-copy (SSC) region of 18,410 bp, and a pair of inverted repeats (IR) regions of 25,966 bp. Complete chloroplast genome contains 135 genes. There were 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The complete genome GC content was 37.3%. To study the phylogenetic relationship of C. octopetala with other members of Theaceae, 19 species (five species of Camellia, two species of Polyspora, one species of Tutcheria, two species of Pyrenaria, one species of Apterosperma, two species of Schima, one species of Franklinia, two species of Gordonia, three species of Stewartia) of Theaceae (Yu et al. 2017), all are from NCBI GenBank. The sequences were aligned by MAFFT v7.307 (Katoh and Standley 2013) and phylogenetic tree constructed by RAxML (Stamatakis et al. 2008) (Figure 1). Camellia octopetala, sister to C. crapnelliana, and genus Camellia is monophyletic group embedded in Theaceae with strong bootstrap support.
Figure 1.
Phylogenetic analysis of 20 species of Theaceae based on plastid genome sequences by RAxML, bootstrap support value near the branch.
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. 19:455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- eFloras. 2008. Camellia octopetala. Flora China. 12:396. [Google Scholar]
- Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res. 41:e129. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X. 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. 41:1–7. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 57:758–771. [DOI] [PubMed] [Google Scholar]
- Wyman S K, Jansen R K, Boore J L.. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20:3252–3255. [DOI] [PubMed] [Google Scholar]
- Yu X-Q, Gao L-M, Soltis DE, Soltis PS, Yang J-B, Fang L, Yang S-X, Li D-Z. 2017. Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. New Phytol. 215:1235–1248. [DOI] [PubMed] [Google Scholar]
- Zhang W, Zhao Y, Yang G, Tang Y, Xu Z. 2017. Characterization of the complete chloroplast genome sequence of Camellia oleifera in Hainan, China. Mitochondr DNA B. 2:843–844. [DOI] [PMC free article] [PubMed] [Google Scholar]