Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution.

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: , , , and . The size of the chloroplast genome ranged from 153,629 bp () to 160,427 bp (). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of , , and were lost in , in that the gene was lost in and In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. had the highest number of repeats (81), while had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in , and, at most, 78 in . Interestingly, we identified 16 genes with positive selection sites (the , , , , , , , , , , , , , , , and genes), which might play an important role in the orchid species' adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions ( intron, -, -, -, and -) and six coding regions (, , , , , and ). The phylogenetic analysis based on whole cp genomes showed that was closely related to var. , while and formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.