Complete Chloroplast Genome of Nine Anoectochilus (Orchidaceae) Species from China: Comparative Analysis and Phylogenetic Significance

Members of Anoectochilus Blume (Goodyerinae, Orchidaceae) are terrestrial and perennial herbs, which possess highly medicinal and ornamental values. The intergeneric relationship and species delimitation of Anoectochilus have been controversial and needed further evidence for clarification. Therefore, complete chloroplast (cp) genomes of nine Anoectochilus species from China were analyzed and compared; three of these were sequenced and assembled here, and the other six species were downloaded from the GenBank. The cp genomes from nine species possessed conserved quadripartite structures. Genome sizes varied between 151,414 bp and 152,976 bp, exhibiting GC contents of 36.8–37.0% and possessing 133 genes. Comparative analysis of these cp genomes indicated higher variation in the single-copy regions. Based on coding sequences (CDSs) from complete cp genomes, phylogenetic analysis revealed that the nine Anoectochilus species formed a monophyletic clade, being a sister group to Rhomboda Lindl., but distant from two species of Odontochilus Blume that was presumed to be related for a long time. Meanwhile, the nine Anoectochilus species were divided into two subclades with strong supports, providing new evidence for the delimitation of some easily confused species.