The complete chloroplast genome of Coelogyne barbata (Orchidaceae), a rare and ornamental orchid

Abstract

The genus of Coelogyne Lindl. comprised about 200 species while its generic relationship has been uncertain. The whole chloroplast genome of C. barbata was reported in order to provide new data on the molecular phylogeny of Coelogyne. The cp genome of C. barbata was 1,600,93 bp in total length, including a pair of inverted repeat regions (IR, 26,710 bp), one large single-copy region (LSC, 87,868 bp), and one small single-copy region (SSC, 188,05 bp). The complete chloroplast DNA encoded 132 genes, containing 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that C. barbata was related to Pholidota imbricata.

Keywords:

• Coelogyne barbata
• chloroplast genome
• Orchidaceae
• phylogenetic analysis

The genus of Coelogyne Lindl. (tribe Arethuseae, subfam. Epidendroideae) comprised about 200 species in which generic relationship had been uncertain (Chase et al. 2015). C. barbata Lindl. ex Griff. was recognized by possessing sparse pseudobulbs with two leaves, hysteranthous inflorescence with white flowers, and margin long fimbriate on the lip. It grew on trees in forests or on cliffs and was distributed in SW China, Bhutan, NE India, and Nepal (Chen and Clayton 2009). Since the plastid genome would provide molecular evidence for plant systematic (Jansen et al. 2007; Nock et al. 2011; Pan et al. 2019), the complete chloroplast genome of C. barbata was reported.

Leaf samples of C. barbata were obtained from Fumin County, Yunnan Province, China (25°20′19″N, 102°27′26″E). The voucher specimen was deposited in the Herbarium of Southwest Forestry University (HSFU, Lilu-20180004). High quality chloroplast genomic DNA of C. barbata was extracted from the fresh leaf by using the modified CTAB procedure (Doyle and Doyle 1987) and sequenced on the Illumina Hiseq 2500 platform (Illumina, San Diego, CA) in Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China). Genome sequences were assembled and screened using GetOrganelle pipe-line (Jin et al. 2018). Then, the new sequence was annotated with Geneious Prime version 2020.1.2 (Kearse et al. 2012). Finally, the chloroplast genome sequence was submitted to GenBank and obtained an access number MT627604.

The complete chloroplast genome of C. barbata was 160,093 bp in length and contained two inverted repeats (IR, 26,710 bp) regions, a large single-copy region (LSC, 87,868 bp), and a small single-copy region (SSC, 18,805 bp). This gene sequence encoded 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Among them, LSC, SSC, and IR regions accounted for 35.2%, 30.5%, and 43.3% of the GC-content. In addition, the overall GC-content was 37.3%. The gene order and organization of C. barbata were consistent with those of Dendrobium species in subfamily Epidendroideae (Wang et al. 2020).

To confirm the phylogenetic position of C. barbata, a maximum likelihood (ML) tree was conducted using RAxML v8.1.11 (Stamatakis 2014) as implemented on the Cyberinfrastructure for Phylogenetic Research (CIPRES) Science Gateway (http://www.phylo.org/, Miller et al. 2010), employing the GTRtG model with 1000 bootstrap iterations (-#/-N). Other parameters used the default settings. Phylogenetic analysis based on 79 protein-coding genes of 10 representative plastomes within the subfamily Epidendroideae as ingroup. According to the updated molecular phylogeny of Orchidaceae (Chase et al. 2015; Li et al. 2016), 10 species from two tribes (Malaxideae Lindl. and Arethuseae Lindl.) in subfamily Epidendroideae were selected as ingroup, while two species from subfamily Orchidoideae as outgroup. It turned out that C. barbata was closely related to Pholidota imbricata Hook. with 100% support (Figure 1).

Figure 1. Phylogenetic position of Coelogyne barbata inferred by maximum likelihood (ML) based on 79 protein-coding genes from 12 species of Orchidoideae. Sequences used in this study were downloaded from the NCBI GenBank database. The bootstrap values are shown next to the nodes.

Acknowledgements

First of all, we were grateful to Dr. Fei Zhao in Kunming Institute of Botany Chinese Academy of Sciences for his help in this article. Second, we were grateful to Mr. Zhi-feng Xu and Mrs. Xiao-yun Wang in the Wild Orchid Conservation Center of Yunnan Fengchunfang Biotechnology Company for providing the materials.

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov, reference number MT627604.

Additional information

Funding

This work was supported by a grant from Science and Technology Department of Yunnan Province in China (Grant No. 2019IB018, Comprehensive Scientific Investigation on Ailaoshan and Wuliangshan Mountains National Park).