Fig. 4

Insertion time frames of wheat LTR retrotransposons. a Persistence rate in number of elements per 10,000 years that have remained intact until now (meaning they have not been removed or truncated over time). The D subgenome has younger flLTR-RTs, the curves for all superfamilies are shifted by ~ 0.5 Myr. The shoulder at 0.5 Myr in the A and B subgenomes could reflect a decrease in removal rates after the tretraploidization. b Comparison of different cluster stringencies. y-axis: subgenome specificity of the clusters, e.g., “ABD” has members from all three subgenomes, “AB” only from A and B; x-axis: log cluster size; the color coding gives the number of clusters; the circle area corresponds to the number of elements. The family clustering at 80% identity over 80% mutual coverage generates large clusters, but has a low proportion of subgenome-specific clusters. The 90/90 subfamily level cluster set with a high number of subgenome-specific clusters and three large ABD clusters was used for further analyses. c Lifespan of subfamilies containing only either A, B, or D members. The line thickness represents cluster size. Lineages unique to the A or B subgenome occur only down to ~ 0.5 Myr, confirming the estimated time point for the tetraploidization. However, D subgenome-unique lineages kept on proliferating, a clear sign for a very recent hexaploidization