The absence of these genes is unlikely to be due to genome assembly problems because 98.66% of the transcripts assembled from transcriptome data could be mapped to the assembly. Another possibility is that several genes were missed due to gene prediction problems. By mapping RNA reads onto the annotated genome, we found that the majority of RNA reads (>86%) from all G. elata tissues could be mapped to annotated exon regions (Supplementary Table 18). This rate of mapping was comparable to that achieved in the well-annotated rice genome and higher than in the P. equestris genome (Supplementary Table 18). Through analysis of gene synteny among G. elata and P. equestris and D. officinale, we detected 2961 gene deletion events in G. elata versus P. equestris, and 3120 gene deletion events in G. elata versus D. officinale (Supplementary Table 19). Further TBLASTN searches of these deleted genes recovered less than 3% of them. Of these genes, fewer than 15% were supported by RNA-seq data (Supplementary Table 19). Both the RNA mapping results and the synteny deletion analysis confirmed that our gene prediction was comprehensive; thus, the possibility of missing gene annotations was low. Finally, PCR amplification of 18 lost genes (atpD, atpG, IhcA, IhcB, psaD, psaF, psaL, psaN, psbO, psbR, psbY, psb27, psb28, petC, petE, ICS, DHAR, and TRX) confirmed that all were absent from the G. elata genome (Supplementary Figs. 8, 9 and Supplementary Table 20). Thus, the global gene losses in G. elata represent evolutionary events, and might be the result of adaption to an obligate mycoheterotrophic lifestyle.