Chloroplast Genome Analysis of Two Medicinal spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification.

Although the medicinal properties of spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of and . The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes' medium variable regions and evaluated the transferability to another 16 species. We constructed phylogenetic trees including 18 species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of and contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in and 26,715 bp , respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera and . The newly developed primers revealed good transferability among the taxa and provided enough variable sites to distinguish and . The two complete cp genomes and the eight new primers of provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of taxa.