Fig. 5

LTR retrotransposon footprints in the evolution of hexaploid wheat. a Evolution of the wheat genome with alternative scenarios and timescales. The dotted rectangles and * time values represent the scenario of A and B giving rise to the D subgenome by homoploid hybridization [37]. The left timescale is based on another estimate based on the chloroplast genome evolution [16]. The dotted horizontal arrows represent the unidirectional horizontal transposon transfers observed in this study. b Phylogenetic tree of the largest 90/90 cluster (6639 copies). c Top2 cluster (5387 copies), d Top3 cluster (4564 copies). The leaves of the tree are colored by the subgenome localization of the respective elements. The majority of the amplifications took place in the diploid ancestors evidenced by the single colored propagation lineages. Each tree contains one or several younger regions with interweaving A and B insertions (marked by ABAB). These younger proliferations only started in the AABB tetraploid, where the new elements inserted likewise into both subgenomes. The joining of the D genome was too recent to have left similar traces yet. The gray asterisks mark D lineages that stem from a B or A lineage