Abstract
Cymbidium bicolor belongs to Orchid family (Orchidaceae), it has high ornamental and traditional medicinal value. The complete chloroplast genome of C. bicolor was sequenced using the Illumina Hiseq platform. The size of the C. bicolor chloroplast genome is 156,528 bp, with an average GC content of 36.8%. This chloroplast genome has containing a large single copy (LSC) region of 85,907 bp, a small single copy (SSC) region of 17,215 bp, and two inverted (IRa and IRb) repeat regions of two 26,703 bp. A total of 124 genes were annotated, including 78 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree indicated that C. bicolor is closely related to C. mannii in the genus Cymbidium based on 16 whole chloroplast genome sequences.
Keywords: Cymbidium bicolor, complete chloroplast genome, Illumina sequencing
Cymbidium bicolor is belong to Orchid family (Orchidaceae), is a perennial herb, it has high ornamental and traditional medicinal value. It distributed in Guangdong, Hainan, Guangxi, Guizhou, and southwest Yunnan provinces in China, and this orchid plant species is also distributed in countries such as Nepal, Bhutan and India. The genus Cymbidium including about 55 species in tropical and subtropical Asia, south to Papua New Guinea and Australia, with 50 species distributed in China (Zhang et al. 2002). Recently, it has been published few Cymbidium species whole chloroplast genomes (Jiang et al. 2019). Here, we first reported complete chloroplast genomes of C. bicolor based on Illumina pair-end sequencing data.
The voucher specimen of C. mannii is stored at the herbarium of Northwest University (108°55′E, 34°15′N, accession no. SK2017200). Total genomic DNA was extracted from leaf tissue using a plant genomic DNA kit (Tiangen Biotech, Beijing, China). The whole-genome sequencing was conducted with 350 bp pair-end reads on the Illumina Hiseq platform (Illumina, San Diego, CA). After trimming, the high-quality paired-end reads were assembled with the program MITObim v1.7 (Hahn et al. 2013) using the C. mannii chloroplast genome sequence as a reference (GenBank accession no. NC021433) (Wang et al. 2017). Annotations were performed using the online program Dual Organellar Genome Annotator (DOGMA) (Wyman et al. 2004). The C. bicolor chloroplast genome sequence was submitted to GenBank (accession no. MN654912).
The chloroplast genome of C. bicolor was 156,528 bp in length and contains a pair of inverted repeats (IRa and IRb) regions of 26,703 bp, the large single-copy (LSC) region and small single-copy (SSC) region of 85,907 and 17,215 bp. A total of 124 genes were successfully annotated containing 78 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes.
To infer the phylogenetic position of C. bicolor, we constructed the phylogenetic tree based on the 16 complete chloroplast genome sequences obtained from NCBI, including six Cymbidium species, eight Orchid species, and two Liliaceae species as outgroups. All of the chloroplast genome sequences were aligned using MAFFT v7.0.0 (Katoh and Standley 2013). The maximum-likelihood (ML) phylogenetic tree conducted using software RAxML (Stamatakis 2006). The phylogenetic tree indicated that C. bicolor is closely related to C. mannii with 100 bootstrap support value (Figure 1). This complete chloroplast genome sequence provides the basis for future research on the evolution and molecular biology of the genus Cymbidium and Orchidaceae species.
Figure 1.
Maximum-likelihood (ML) phylogenetic tree based on 16 complete chloroplast genome sequences. The accession numbers are shown in the figure, and the triangle indicates the species C. bicolor sequenced in this study.
Funding Statement
This work was supported by the Functional traits of plant communities at different elevation gradients in the Taibai Mountain of Qinling Mountains financed by the Ministry of Science and Technology of China #1 under Grant no. [2016YFC0500202]; the Public health specialty in the Department of traditional Chinese Medicine #2 under Grant nos. [2016-44, 2017-66, 2018-43, and 2019-68].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- 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(13):e129. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jiang YT, Lin RQ, Liu B, Zeng QM, Liu ZJ, Chen SP. 2019. Complete chloroplast genome of Cymbidium ensifolium (Orchidaceae). Mitochondrial DNA B. 4(2):2236–2237. [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(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. [DOI] [PubMed] [Google Scholar]
- Wang X, Yang N, Su J, Zhang H, Cao X. 2017. The complete chloroplast genome of Gentiana macrophylla. Mitochondrial DNA B. 2(2):395–396. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255. [DOI] [PubMed] [Google Scholar]
- Zhang MY, Sun CY, Hao G, Ye XL, Liang CY, Zhu GH. 2002. A preliminary analysis of phylogenetic relationships in Cymbidium (Orchidaceae) based on nrITS sequence data. Acta Bot Sin. 44:588–592. [Google Scholar]