Complete Chloroplast Genome of Two Papilionanthe (Aeridinae, Epidendroideae, Orchidaceae) Species: Comparative Analysis and Phylogenetic Insights

Papilionanthe Schltr. (Vandeae, Epidendroideae, Orchidaceae) is distinguished by its terete leaves and showy flowers, with significant horticultural and medicinal values. However, its systematic position in Aeridinae has been controversial and not been paid attention to or clarified. This study is focused on the complete chloroplast (cp) genomic data of P. biswasiana and P. teres in order to provide some genomic data for its phylogenetic relationship. The cp genomes of two Papilionanthe were 148,183 bp (P. biswasiana) and 148,145 bp (P. teres) in length, with similar GC content (36.5–36.6%). Comparative cp genomes of two Papilionanthe species and the other eight related taxa revealed differences in sequence analysis and statistics. A phylogenetic analysis based on CDS from complete cp genomes supported the notion that Papilionanthe is a monophyletic clade and closer to Luisia than to Paraphalaenopsis. It was obvious that there are four well-supported clades in Aeridinae, which could hold a significant implication for the phylogenetic relationship between Papilionanthe and other alliances in Aeridinae. Furthermore, the taxonomic positions of V. flabellata and H. himalacia were also reconfirmed herein by phylogenetic analysis of the cp genomes.