Proteins of G. elata, P. equestris and D. officinale were aligned using the BLASTp algorithm (E-value < 1e−7). Alignments with matches of at least 30% identity and coverage higher than 30% were retained for comparison. The best reciprocal BLAST pairs between different genomes were extracted as putative orthologous gene pairs. Then, using gene location information in each species, we identified micro-synteny gene blocks between G. elata and the other two orchids. Putative gene loss events were traced from the synteny table using the flanking gene method. Given three genes A, B, and C in order, if gene A and C were presented as collinear orthologs in two genomes, but B was missed in one of the genome (for example, G. elata), then gene B was denoted as a possible lost gene in G. elata. To avoid false positives due to the failure of gene annotation, the G. elata intergenic genomic sequence between A and C was extracted, and a GeneWise prediction in this intergenic region was carried out using the B protein sequence from P. equestris as seed. If the predicted protein could be aligned to the seed protein with coverage >70%, and did not contain frameshift or premature stop codon mutations, this gene loss event was defined as a false positive and filtered out (Supplementary Table 19).