We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

Mycorrhizal fungi are central to the biology of land plants. However, to what extent mycorrhizal shiftsbroad evolutionary transitions in root-associated fungal symbiontsare related to changes in plant trophic modes remains poorly understood.We built a comprehensive DNA dataset of Orchidaceae fungal symbionts and a dated plant molecular phylogeny to test the hypothesis that shifts in orchid trophic modes follow a stepwise pattern, from autotrophy over partial mycoheterotrophy (mixotrophy) to full mycoheterotrophy, and that these shifts are accompanied by switches in fungal symbionts.We estimate that at least 17 independent shifts from autotrophy towards full mycoheterotrophy occurred in orchids, mostly through an intermediate state of partial mycoheterotrophy. A wide range of fungal partners was inferred to occur in the roots of the common ancestor of this family, including 'rhizoctonias', ectomycorrhizal, and wood-or litter-decaying saprotrophic fungi. Phylogenetic hypothesis tests further show that associations with ectomycorrhizal or saprotrophic fungi were most likely a prerequisite for evolutionary shifts towards full mycoheterotrophy.We show that shifts in trophic mode often coincided with switches in fungal symbionts, suggesting that the loss of photosynthesis selects for different fungal communities in orchids. We conclude that changes in symbiotic associations and ecophysiological traits are tightly correlated throughout the diversification of orchids.

1. Orchid mycorrhiza forms unique symbiotic associations between members of the Orchidaceae and multiple ecological guilds of fungi. Because orchids associate with a wide variety of fungi with different ecological functions, they represent an ideal study system to address fundamental questions about the evolution and ecophysiology of mycorrhizal symbiosis. Although it is well established that shifts in mycorrhizal associations are linked to transitions in plant trophic mode, it remains unclear what ecological drivers promote these evolutionary changes.2. Here, we investigated mycorrhizal communities and isotope signatures across six populations of the terrestrial orchid Neottia ovata growing under contrasting light conditions in temperate Europe. We hypothesized that plants growing in forests would associate with different mycorrhizal fungi than plants occurring in grasslands and that the limited light availability in forests leads to a higher contribution of fungi to the carbon budget of orchids.3. Our results showed that N. ovata predominantly associated with rhizoctonia fungi of the family Serendipitaceae in both habitats, but plants in forests also recruited ectomycorrhizal fungi. Root communities highly resembled soil communities and variation in root communities was significantly related to habitat type and edaphic factors. In contrast, isotope signatures ( 13 C, 15 N, 2 H and 18 O) and N concentration showed no significant relationship with habitat type. In addition, both 13 C and 2 H were not significantly correlated to habitat's light availability. 4.Although it has been suggested that the presence of a wide variety of ectomycorrhizal fungi in root communities of orchids can serve as a precursor for evolutionary shifts to partial mycoheterotrophy (mixotrophy), the presence or absence of | 1949Functional Ecology WANG et al.