Characterization and Phylogenetic Analysis of the First Complete Chloroplast Genome of (Orchidaceae: Orchideae)

Background: Genomic analysis is crucial for better understanding the evolutionary history of species and for their conservation. is a rare medicinal plant endemic to China. However, the complete chloroplast genome of this species has not been reported to date. Insufficient genomic research on has hindered effective conservation efforts for this valuable plant.

Methods: In this study, we sequenced and assembled the first complete chloroplast genome of using Illumina sequencing technology. We conducted a comparative analysis of its chloroplast genome with related species and reconstructed phylogenetic relationships.

Results: The chloroplast genome of exhibited a typical quadripartite structure with a length of 158,658 bp. A total of 123 genes, 118 simple sequence repeats, and 51 dispersed repetitive sequences were identified. The inverted repeat boundaries were significantly expanded, along with the pseudogenization and loss of multiple NDH genes. Codon usage bias is primarily influenced by natural selection and other factors, with the gene under positive selection. Additionally, 10 hypervariable regions were detected for species identification and evolutionary studies. Phylogenetic analysis indicated that and form a clade, with as their sister species, located at the basal position of the - alliance.

Conclusions: The chloroplast genome structure and gene content of exhibit certain degrees of variation compared to other species within the Orchidinae subtribe. This genome should be useful for further investigations into the biology of and the development of biodiversity conservation strategies.