Fig. 3

Distribution of different subfamilies in the A, B, and D subgenomes. a Distribution of RLC_famc1 (Fatima) retrotransposons. Group 6 chromosomes were chosen as representative for the whole genome. A phylogenetic tree of the different subfamilies is shown at the left. For the construction of the phylogenetic tree, the LTR sequences were used (internal domains between RLC_famc1.1 and the other subfamilies are completely different, as only RLC_famc1.1 contains reverse transcriptase and integrase genes). Bootstrap values (100 repetitions) are indicated. Sequence organization and gene content of the individual subfamilies are shown to the right of the tree. Chromosomal distributions are shown at the right in bins of 50 Mb as heat-maps and bar plots to indicate absolute numbers. The y-axis indicates the total number of kb that is occupied by the respective subfamily in each bin. The most recently diverged subfamilies RLC_famc1.4 and RLC_famc1.5 show strong differences in abundance in different subgenomes. b Examples of TE subfamilies that have strongly differing copy numbers in the A, B, and D subgenomes. Again, only a single group of homeologous chromosomes is shown (see Additional file 1: Figures S1–S3 for the other chromosomes). Abundance is shown in 30-Mb windows