Both pseudogenizations and genome rearrangements contributed to the gene lost process of G. elata. We found 876 and 1080 pseudogenes in G. elata using P. equestris and D. officinale genes as seeds, respectively (Supplementary Tables 21–24). Through a whole-genome alignment between G. elata and P. equestris, we found 487 genes were lost due to local rearrangements (SV genes, Supplementary Tables 25 and 26). Functional genes in G. elata were located closer to transposable elements than to pseudogenes and SV genes, suggesting that transposable element did not play significant role during the gene lost processes in G. elata (Supplementary Fig. 10). Thus the gene lost processes in G. elata might be dominated by random mutations as we found many pseudogenes in G. elata. Notably, compared with the genomes of P. equestris, D. officinale, A. comosus (pineapple, used in this study as an outgroup) and Arabidopsis thaliana (used in this study as an outgroup), the G. elata genome has a reduced number of genes related to plant resistance to pathogens, such as the NBS (the nucleotide-binding site) gene family, PR (pathogenesis-related) gene family, and genes of antioxidant proteins (Fig. 1d, Supplementary Fig. 11 and Supplementary Table 27). For example, the ICS gene, which is known to function as a primary modulator of salicylic acid-based plant defense responses13, is absent from the G. elata genome, illustrating the loss of a key gene for systemic acquired resistance (Supplementary Figs. 8, 9 and Supplementary Table 27).