Much of the G. elata genome (66.18%) was occupied by transposable elements (TEs). Class I (retrotransposons) and Class II (DNA transposons) TEs accounted for 55.94% and 4.38% of the genome, respectively (Supplementary Table 6). Long terminal repeats (LTRs) formed the most abundant category of TE, with LTR/Gypsy and LTR/Copia occupying 45.04% and 7.10% of the genome, respectively (Supplementary Table 7). Global activity of LTRs was similar between G. elata and Phalaenopsis equestris, while Dendrobium officinale presented a recent burst of LTR activities (Supplementary Fig. 2a). Compared to P. equestris, all LTR families in G. elata had fewer members, except a substantive expansion of del family (Supplementary Table 8 and Supplementary Fig. 2b). Through a combination of ab initio prediction, homology search, and RNA sequence-aided prediction, 18,969 protein-coding genes were predicted in the G. elata genome. Of these genes, 81.6% were functionally annotated (Supplementary Table 9) and 88.69% had detectable transcripts in an RNA-seq analysis of protocorms, tubers (juvenile, immature, and mature tubers), and scapes (Supplementary Table 10). Our transcriptomics analysis revealed that there were 10,548 differentially expressed genes among the five growth stages; these differentially expressed genes clustered into five distinct groups that were representative of the particular stages of growth of G. elata (Supplementary Fig. 3, Supplementary Table 11 and Supplementary Note).