The complete chloroplast genome sequence of Calanthe delavayi (Orchidaceae), an endemic to China

Abstract

Calanthe delavayi, an endemic terrestrial orchid distributed in southwestern China. In this study, the complete chloroplast genome (cpDNA) sequence of C. delavayi was determined from Illumina pair-end sequencing data. With a total length of 150,181 bp in length and includes two inverted repeat regions (IRs) of 23,721 bp each, which were separated by a large single copy region (LSC) 87,392 bp and a small single copy region (SSC) 18,693 bp. The chloroplast genome contained 135 genes, including protein-coding genes, tRNA genes, and eight rRNA genes. Phylogenetic analysis indicates that C. delavayi, C. davidii, and C. triplicata cluster together, placed them within tribe Collabieae.

Keywords:

• Chloroplast genome
• phylogenetic
• Illumina sequencing
• Calanthe delavayi

Calanthe delavayi Finet is an alpine plant endemic to temperate zones of southwestern China at 2700–3500 m (Perner and Cribb 2002; Chen et al. 2010). On the basis of its floral morphology, the specie was treated as a member of genera Phaius in Pridgeon et al. (2005), but it was confirmed as a member of genera Calanthe due to molecular evidence by Zhai et al. (2014). Calanthe delavayi has become a key species in the study of taxonomy owing to its complex taxonomic history between Calanthe and Phaius, meanwhile Calanthe (∼216 species) and Phaius (∼45 species) are two biggest genera in tribe Collabieae (Clayton and Cribb 2013; Chase et al. 2015), at present, there are uncertainties in the classification of tribe Collabieae. To better understand of its evolution history and genetic information, we characterized the complete chloroplast genome sequence of C. delavayi as a resource for future genetic studies.

The total genomic DNA was extracted from dry leaves using a modified CTAB method (Doyle and Doyle 1987) and sequenced based on the Illumina pair-end technology. The leaf sample was collected from Huanglong Valley, Huanglong Nature Reserve, Sichuan, China (N 32°45′, E 103°49′) and the DNA stored at the Fujian Agriculture and Forestry University (N0.S42). The clean reads were firstly aligned to C. triplicata (GenBank accession No. KF753635) (Yang et al. 2014) and then assembled into contigs in the software CLC Genomics Workbench v8.0 (CLC Bio, Aarhus, Denmark). The assembled chloroplast genome was annotated using DOGMA, and the annotation was corrected using Geneious (Kearse et al. 2012). The physical map of the new chloroplast genome was generated using OGDRAW (Lohse et al. 2013). The accurate new annotated complete chloroplast genome was submitted to GenBank with accession number MK388860. The complete chloroplast genome of C. delavayi is 150,181 base pairs (bp) in length, containing a large single-copy (LSC) region of 83,559 bp, a small single-copy (SSC) region of 16,486 bp, and two inverted repeat (IR) regions of 25,068 bp. The new sequence possesses total 135 genes, of which 114 were unique genes, including 73 protein-coding genes, eight rRNA genes, and 40 tRNA genes. Among all of these genes, eight rRNA genes (i.e. 4.5S, 5S, 16S, and 23S rRNA), eight protein-coding genes (i.e. ndhB, rpl2, rpl23, rps12, rps19, rps7, ycf15, and ycf2), and 10 tRNA genes (i.e. trnA-UGC, trnH-GUG, trnI-CAU, trnI-GAU, trnL-CAA, trnM-CAU, trnN-GUU, trnR-ACG, trnS-UGA, and trnV-GAC) occur in double copies. The overall GC-content of the whole plastome is 36.9%, whereas the corresponding values of the LSC, SSC, and IR regions are 34.5, 29.4, and 43.3%, respectively.

The phylogenetic analysis was carried out with C. delavayi and 16 other complete cp genome of species from Orchidaceae, comprising of 14 Epidendroideae species (Bletilla ochracea, Calanthe triplicata, Calanthe davidii, Cymbidium ensifolium, Erycina pusilla, Eulophia zollingeri, Cattleya crispata, Corallorhiza mertensiana, Masdevallia coccinea, Dendrobium catenatum, Oberonia japonica, Epipactis mairei, Sobralia callosa, and Gastrochilus fuscopunctatus,) and two Orchidoideae species (Anoectochilus emeiensis and Goodyera fumata) as outgroup. The sequences were aligned using HomBlocks pipeline (Bi et al. 2018). RAxML-HPC2 on XSEDE version 8.2.10 (Stamatakis 2014) was used to construct a maximum likelihood tree, the branch support was computed with 1000 bootstrap replicates. C. delavayi, C. davidii, and C. triplicata cluster together with strong bootstrap support placed them within the tribe Collabieae (Figure 1).

Figure 1. Maximum likelihood tree based on the complete cp genome sequences of 17 species from the Orchidaceae, with Anoectochilus emeiensis and Goodyera fumata as outgroup. Shown next to the nodes are bootstrap support values based on 1000 replicates.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by Outstanding Youth Fund of Fujian Agricultural and Forestry University (XJQ201504) and the National Natural Science Fund (31400180).