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LTR retrotransposons were distributed unevenly throughout each chromosome.

These results show that the different wheat A genomes experienced large-scale structural rearrangements both before and after polyploidization with other genomes, and have experienced independent gain or loss of LTR retrotransposons after the polyploidization event.

A customized script was implemented to identify intact LTR/Copia and LTR/Gypsy retrotransposons.

Together, these differences may contribute to the larger size of Ta3B in comparison to Tu3, and suggest that amplification of LTR retrotransposons after the divergence of the A and B genomes may be relevant for wheat genome evolution.