Plastome analysis elucidates the phylogenetic placement of the mycoheterotrophic genus Yoania (Orchidaceae) and its plastomic degeneration during the evolution of mycoheterotrophy

Abstract Subtribe Calypsoinae (Epidendroideae, Orchidaceae) comprises several fully mycoheterotrophic species. Phylogenetic analysis indicates that full mycoheterotrophy has evolved independently at least four times within this group, including the Yoania clade. The taxonomic classification of Yoania species has been challenging. Therefore, to understand the plastomic degeneration during the evolution of mycoheterotrophy and to uncover the phylogenetic relationship within Yoania, we conducted a phylogenetic analysis using eight specimens representing all six recognized Yoania taxa from the complete plastome and partial ribosomal DNA (rDNA) operon sequence (ETS–18S–ITS1–5.8S–ITS2–26S). Among the Calypsoinae taxa examined, Yoania possessed the shortest plastome, ranging from 43 998 to 44 940 bp. Comparative analysis of the plastomes revealed a relatively conserved gene structure, content, and order, with species-level sequence variation (in the form of indels) primarily observed in the intergenic spacer regions. Plastomic gene-block inversions were observed between Yoania and Danxiaorchis singchiana, but not between Yoania and other related genera. Phylogenetic analyses based on the plastome and rDNA data strongly supported the monophyletic placement of Yoania within Calypsoinae, and indicated substantial molecular divergence between Yoania and other Calypsoinae taxa. Yoania can thus be considered genetically isolated from the other Calypsoinae taxa.