Compared to P. equestris (29,431 protein-coding genes) and D. officinale (28,910 protein-coding genes), G. elata has a relative small proteome size (18,969 protein-coding genes). The estimated proteome size of G. elata is the smallest theoretical proteome so far identified among angiosperm genomes (Supplementary Table 12). Comparison of G. elata, P. equestris, and D. officinale genes that have functional annotation information revealed global gene set reduction in the G. elata genome. For example, almost all second level gene ontology (GO) categories had fewer genes in G. elata than in the other two species, and 9 of these categories (16.7%) were significantly reduced (Fisher’s Exact test, p < 0.05, Supplementary Fig. 6 and Supplementary Table 13). We also found that several Pfam domain families were significantly reduced in the G. elata genome (Supplementary Table 14). Among the 14 angiosperm used in the phylogenetic analysis, G. elata had the lowest number of gene families; moreover, G. elata had on average the lowest number of genes in each gene family (Fig. 1c, and Supplementary Table 15). This consistently low number of genes and gene families suggests that many gene families have been eliminated from the G. elata genome, and further suggests that many of the remaining gene families have contracted. Gene family expansion and contraction analysis based on maximum likelihood modeling of gene gain and loss confirmed that 3586 gene families had undergone contraction in G. elata, much more compared to the other two orchid genomes (Supplementary Fig. 7 and Supplementary Table 16). A Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis, which assessed 956 orthologous groups with genes present as single-copy in at least 90% of plant genomes12, revealed that 195 (20.4%) highly-conserved genes were missing from the G. elata genome. This rate of absence is much higher than in the genomes of the 13 land species that were included in this analysis (Supplementary Table 17). All of these analyses indicate that G. elata has undergone extensive gene losses, even for genes that were conserved in other plant species that have also undergone extensive lost events.