The complete chloroplast genome of Changnienia amoena S. S. Chien (Orchidaceae) and its phylogenetic implication.

Changnienia amoena S. S. Chien is mainly distributed in the mid-subtropical hilly areas of central and eastern China at an altitude of 200-1700 m. It has important academic significance in the orchid phylogeny, and is an excellent wild flower and precious medicinal plant. The species was once abundant but has become rare and endangered in recent years and has been identified as Endangered (EN) under criteria A2c (The IUCN Red List and Threatened Specis) because of the habitat fragmentation and unduly commercial collections. In this study, the complete chloroplast (cp) genome sequence of C. amoena was determined using next-generation sequencing. The entire cp genome was determined to be 156,818 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 84,847 and 18,141bp, respectively, which were separated by a pair of 26,915 bp inverted repeat (IR) regions. The genome contained 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes.The overall GC content of the genome is 37.1%. A phylogenetic tree reconstructed by 48 chloroplast single-copy coding gene reveals that C. amoena is closely related with Calypso bulbosa.