The complete chloroplast genome sequences of Anoectochilus nandanensis and A. calcareus

Abstract

Anoectochilus nandanensis and A. calcareus are medical plants with important economic value. In this study, we assembled their complete chloroplast (cp) genome sequences. The assembled cp genomes are 152,415 bp and 151,864 bp in length, including a large single-copy (LSC) region of 82,412 bp and 82,083 bp, a small single-copy (SSC) region of 17,367 bp and 17,142 bp and a pair of inverted repeats (IRs) of 26,318 bp and 26,320 bp, respectively. All genomes contained 133 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content of genomes in both species is 36.9%. Further phylogenetic analysis showed that three Anoectochilus comprised of a monophyletic clade and A. nandanensis was more close to A. emeiensis.

Keywords:

• Anoectochilus nandanensis
• A. calcareus
• chloroplast genome
• phylogenetic analysis

The Anoectochilus genus in Orchidaceae includes about 40 species (Editorial Committee of Flora of China 2009; Qu et al. 2015), in which Anoectochilus calcareus Aver. and Anoectochilus nandanensis Y. Feng Huang & X. C. Qu are local medical plants with important economic value. However, chloroplast sequence variations of these two species remain unclear. In this study, complete chloroplast genomes of A. nandanensis and A. calcareus were sequenced and analyzed for improving the understanding of their genetic variations, which will serve effective conservation and utilization of its genetic resources. Each sample of A. nandanensis and A. calcareus were collected from fresh leaves of only one individual. Voucher specimens (Yunfeng Huang 201901113, Yunfeng Huang 201901114) were collected from Guangxi for A. nandanensis (N24°59′7.44″, E107°56′28.68″, 640 m) and A. calcareus (N23°0′19.44″, E105°51′55.54″, 1113 m) and deposited in the Herbarium of Guangxi Institute of Traditional Medical and Pharmaceutical Science (GXMI). The total DNA was extracted using the modified CTAB method (Doyle 1987). DNA data were sequenced using the Illumina Hiseq 2500 platform (Illumina, San Diego, CA, USA). Subsequently, chloroplast genome assembly using GetOrganelle (Jin et al. 2018) and the annotation was performed with PGA (Qu et al. 2019), then confirmed manually. Finally, the complete chloroplast genome was deposited in GenBank (accessible numbers: MT021458 and MT021459).

The complete chloroplast genomes of A. nandanensis and A. calcareus were 152,415 bp and 151,864 bp in length, respectively. They exhibit the typical quadripartite structure, including a pair of IRs (26,318 bp and 26,320 bp, respectively) separated by the LSC (82,412 bp and 82,083 bp, respectively) and SSC (17,367 bp and 17,142 bp, respectively) regions. Each of them contains 113 unique genes, including 79 protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. Twenty genes were duplicated in the IRs, giving a total of 133 genes. Overall, GC contents of the whole chloroplast genomes from both A. nandanensis and A. calcareus are 36.9%.

In order to clarify their phylogenetic relationships, we further used the software RAxML to construct a phylogenetic tree with 1000 bootstraps under the GTRGAMMA substitution mode (Stamatakis 2014). Twenty six complete chloroplast genomes in Orchidaceae and one outgroup were selected in this study, including three Anoectochilus species. All these sequences were aligned using the software MAFFT v.7 (Katoh and Standley 2013). Our phylogenetic analysis showed that three Anoectochilus species comprised of a monophyletic clade and A. nandanensis was more close to A. emeiensis (Figure 1).

Figure 1. ML phylogeny recovered from 27 complete chloroplast genomes sequences by RAxML. NCBI accession number is shown after each species name.

Disclosure statement

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

Additional information

Funding

This work was supported by Biodiversity Survey, Observation and Assessment Program of Ministry of Ecology and Environment of China (8-3-7-20-5); Major project of the central government of China [No. 2060302-1605-03].