Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus and provides insights into plastid gene degeneration.

The orchid genus R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. . This study examined plastome degeneration in in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. . Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. is the sister lineage to sect. , the only leafy autotrophic species in sect. , was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. . The comparative assessment of plastome structure and gene degradation in revealed that plastid genes were pseudogenised or physically lost in all species, including in leafy autotrophic species of both sections. Levels of plastid gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.