The complete chloroplast genome of Liparis nervosa (Orchidaceae).

Liparis nervosa, a terrestrial orchid was widely used as a traditional medicinal plant in China. In this study, we assembled the complete chloroplast genome of L. nervosa using Illumina sequencing data. The whole genome is 158,716 bp, contains a large single-copy region (LSC 86,010 bp), a small single-copy region (SSC 18,276 bp), and a pair of inverted repeats (IR 27,215 bp). The complete genome has 132 genes, including 77 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. In addition, a maximum-likelihood phylogenetic analysis demonstrated that L. nervosa was most closely related to Oberonia japonica. This work provides a theoretical basis for the development of conservation strategies of L. nervosa.

Liparis nervosa is an herbaceous plant belonging to the Orchidaceae family (Wu and Raven, 2009). It is a terrestrial orchid widely distributed in the tropical and subtropical regions of the world. In China, L. nervosa was used as a traditional medicinal plant for detoxicating and hemostatic functions for a long history. Previous studies have shown that various nervogenic acid derivatives, pyrrolizidine alkaloids, and active phenanthrenes were isolated from L. nervosa and they have antihypertensive, hypolipidemic, pro-coagulant, and antitumor activity (Huang et al. 2013; Song et al. 2013; Liu et al. 2016; Lin et al. 2018). However, due to the artificial exploitation and the destruction of the habitat, L. nervosa has become an endangered plant species in the China Species Red List (Wang and Xie 2004). The complete chloroplast genome of L. nervosa was assembled and annotated in this paper. The research not only will provide a support for in-depth study of L. nervosa, but also is helpful to lay a theoretical basis for the development of conservation strategies.

The samples of L. nervosa were collected from Qinglong waterfall scenic area, Yongtai, Fujian province, China (25°45′22.37″N, 118°57′48.36″E). The specimens are kept in the Herbarium of Fujian Agriculture and Forestry University (specimen code FAFU01847).

The total genomic DNA was extracted from leaves using a modified CTAB method (Doyle and Doyle 1987) and sequenced by the BGISEQ-500 platform. The clean reads were used to assemble the complete chloroplast genome and then annotated with the chloroplast genome of Bletilla ochracea (GenBank accession NC_029483) as the reference sequences. The assembly and annotation methods are described in detail in Ai et al. (2019). Finally, we obtained a complete chloroplast genome of L. nervosa and submitted to GenBank with accession number MN641753.

The complete chloroplast genome of L. nervosa is 158,716 bp in length with the GC-content of the whole plastome 36.9%. It consists of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions of 86,010 bp, 18,276 bp, and 27,215 bp, respectively. The new sequence has a total of 132 genes, including 77 protein-coding genes, 38 tRNA genes, and 8 rRNA genes.

In order to confirm the phylogenetic position of L. nervosa, a phylogenetic analysis was performed based on 12 complete chloroplast genomes of Orchidaceae species, including Dendrobium xichouense (NC_035341), D. fanjingshanense (NC_035344), D. primulinum (NC_035321), Oberonia japonica (NC_035832), Cymbidium sinense (NC_021430), C. ensifolium (NC_028525), Bletilla ochracea (NC_029483), Eulophia zollingeri (NC_037212), Pleione bulbocodioides (NC_036342), Epipactis mairei (NC_030705), Neottia acuminata (NC_030709), and Goodyera schlechtendaliana (NC_029364). All the sequences were downloaded from NCBI GenBank and aligned using MAFFT v7.307 (Katoh and Standley 2013). The phylogenetic tree was constructed by using a maximum likelihood analysis of MEGA 6.0 (Tamura et al. 2013) with 1000 bootstrap replicates. The results indicated that L. nervosa was most closely related to O. japonica (Figure 1).

Figure 1.

Phylogenetic tree constructed based on 12 complete chloroplast genome sequences of Orchidaceae. All the reference sequences were downloaded from NCBI GenBank.