Gastrodia 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