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

Stephanie Goedderz (Australian Tropical Herbarium, James Cook University, Cairns and University of Hohenheim, Germany); Mark A. Clements (Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), Canberra); Stephen J. Bent (Data61 (CSIRO), Brisbane); James A. Nicholls (Australian National Insect Collection (CSIRO) Canberra); Vidushi S. Patel (National Research Collections Australia (CSIRO), Canberra); Philipp M. Schlüter (University of Hohenheim, Germany); Katharina Nargar ( Australian Tropical Herbarium, James Cook University, Cairns and National Research Collections Australia (CSIRO), Canberra).

The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found sect. Leopardanthus as sister lineage to sect. Dipodium. The leafy autotrophic species within sect. Dipodium (D. ensifolium) was found sister to all leafless, mycoheterotropic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence time estimations found that Dipodium diversified ca. 11.3 Ma in the mid Miocene and the origin of mycoheterotrophy in the genus was estimated to have occurred in the late Miocene ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure in Dipodium revealed different degrees of plastid gene degradation of ndh genes within the genus, which ranged from moderately pseudogenised to physically lost, including leafy autotrophic species of both Dipodium sections. Our study showed that Dipodium exhibits an early stage of plastid genome degradation in which all species have retained a full set of functional photosynthesis-related genes and housekeeping genes.