Gastrodia elata (Orchidaceae) is an orchid popularly used in traditional Chinese medicine that has a fully mycoheterotrophic lifestyle with highly reduced leaves and bracts in scape, although field guides and systematists often refer to the plants as leafless4,5. During its life cycle, in associates with at least two types of fungi: Mycena for seed germination and Armillaria mellea for plant growth. To obtain nutrition, it forms an association with A. mellea6 and more than 80% of its ~36-month lifespan is spent underground as a tuber (Fig. 1a). These features of the plant are putative adaptions to its obligate mycoheterotrophic lifestyle. G. elata thus offers the possibility of obtaining a valuable insight into the genetic basis of mycoheterotrophy. Here we present a high-quality reference genome assembly of G. elata (Orchidaceae), and use it to investigate the molecular basis of its full mycoheterotrophic life cycle. The observations presented here will be of value for functional ecological studies seeking to understand the mechanisms and evolutionary basis of plant–fungal associations.Fig. 1Gastrodia elata life cycle and gene-family contraction. a The main developmental stages of G. elata. Seeds develop into a protocorm stage without requiring A. mellea (A). The protocorm then differentiates into a corm stage after commencing its association with A. mellea; note that lateral buds develop into juvenile tubers (B). Young and immature tubers (C). Mature tuber with an emergent young scape (D). Scape (stem and inflorescence) of mature plants (E). b Phylogenetic tree of 14 plant species including G. elata. The red dot represents a calibration point determined from the timetree website. c Bar graph of the number of protein-coding genes in each of the species. Single-copy orthologs include common orthologs with one copy in specific species. Multi-copy orthologs include common orthologs with multiple copy numbers in specific species. Other orthologs include genes from families shared in 2–13 species. ‘Eudicot’ clusters with eudicots. ‘Monocots’ clusters with monocotyledonous plants. ‘Orichd’ clusters with G. elata, P. equestris, and D. officinale. ‘Unclustered’ include genes that cannot be clustered into gene families. d Analysis of gene numbers in the genomes of four species for the nucleotide-binding site gene family (NBS), the pathogenesis-related protein (PR) family (Gel G. elata, Peq P. equestris, Dof D. officinale, Aco A. comosus). Numbers in circles represent the number of family members in each genome, and numbers with plus or minus signs indicate, respectively, the number of duplicated or deleted genes. e The plastid genomes of P. equestris (outer circle) and G. elata (inner circle). Red, protein; orange, rRNA; green, tRNA; gray, genes lost from the plastid genome of G. elata