Intact Long terminal-repeat retrotransposons (LTR) were identified by searching the genomes of G. elata, D. officinale and P. equestris with LTRharvest39 from Genome Tools v1.5.1. The candidate sequences were filtered by two-step procedure to reduce false positives. First, LTRdigest40 was used to identify the primer binding site (PBS) motif based on the predicted tRNA sequences from tRNAscan-SE41, and only elements contained PBS were retained; then protein domains (pol, gag and env) in candidate LTR retrotransposons were identified by searching against HMM profiles collected by Gypsy Databas (GyDB)42. Elements contained gag domain, protease domain, reverse transcriptase (RT) domain and integrase domain, which were considered as intact. Second, families of these intact LTR retrotransposons were clustered using the previously described method43. Finally, LTRs that did not contain protein domains or that belonged to families with less than 5 members were discarded. The EMBOSS program distmat44 was used to estimate LTR divergence rates between the 5′- and 3′- LTR sequences of the intact LTRs (Supplementary Fig. 2).