We also sequenced and assembled the plastid genome of G. elata. We found that the plastid genome of G. elata (35,326 bp) was dramatically restructured and reduced in size, in a similar manner to the reduction in gene number observed for the nuclear genome (Fig. 1e), compared to the plastid genomes of P. equestris (148,958 bp)15 and D. officinale (152,221 bp)16, the two other orchid species with sequenced genomes. The plastid genomes of these two species comprise two single-copy regions (a large and a small single-copy region) and the two identical large inverted repeats (IRs) encode 75 and 76 genes, respectively, that are most associated with photosynthesis. The G. elata plastid genome has lost one IR and encodes only 19 protein-coding genes (Fig. 1e), suggesting that G. elata is an ancient mycoheterotroph and that its plastid genome is in the last stage of a ‘degradation ratchet’, i.e., retention and loss of the five core nonbioenergetic genes17,18. Excluding the possibility that these genes were missed by our genome assembly, the transcriptome sequencing analysis indicated that none of the deleted plastid or nuclear encoded genes were expressed in G. elata, while the five core nonbioenergetic genes, trnE, aacD, clpP, ycf1, and ycf2, were moderately to highly expressed in all five stages in G. elata (Supplementary Tables 30, 31). These results clearly show that both the plastid and nuclear genomes of G. elata have lost most of the genes required for photosynthesis, although the highly degraded plastome is still essential for this full mycoheterotroph.