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Am, Amborella trichopoda; At, Arabidopsis thaliana; Bd, Brachypodium distachyon; Gr, Gossypium raimondii; Si, Setaria italica; Mu, Musa acuminata; Os, Oryza sativa; Pe, Phalaenopsis equestris; Pb, Pyrus bretschneideri; Sb, Sorghum bicolor; Sm, Selaginella moellendorffii; Vv, Vitis vinifera; Zm, Zea mays. For all species, information on the data used can be found in the Supplementary Note and Supplementary Table 22. TEs were extracted from the original data set, and proportions were calculated accordingly.