Fig. 2

Variability and similarity of the repeat composition of the three wheat subgenomes. a Example of sequence alignment of three homeologous regions of ca. 300 kb on chromosomes 3A (from 683.185 to 683.435 Mb), 3B (from 723.440 to 723.790 Mb), and 3D (from 546.330 to 546.700 Mb). Genes red boxes, TEs blue boxes. Sequences sharing > 90% identity over more than 400 bp are represented by red (+/+ strand matches) and blue (+/− strand matches) areas. It shows the high conservation between homeologous genes and collinearity between A-B-D, and it shows the absence of TEs in syntenic positions while intergenic distances tend to be similar between homeologs. Similarities observed between TEs are not collinear and thus strongly suggest independent insertions, in the three subgenomes, of TEs from the same family instead of homeologous relationships. b Proportions of the 20 most abundant TE families comprising the hexaploid wheat genome depicted as fractions of A, B, and D subgenomes. For each family, the A-B-D fractions are represented in green, violet, and orange, respectively. 1 RLC_famc1 (Angela WIS); 2 DTC_famc2 (Jorge); 3 RLG_famc2 (Sabrina Derami Egug); 4 RLG_famc1 (Fatima); 5 RLG_famc7 (Erika Sumana Sumaya); 6 RLG_famc5 (WHAM Wilma Sakura); 7 RLG_famc3 (Laura); 8 RLG_famc4 (Nusif); 9 RLG_famc11 (Romana Romani); 10 RLG_famc10 (Carmilla Ifis); 11 RLC_famc3 (Claudia Maximus); 12 RLG_famc13 (Latidu); 13 RLG_famc6 (Wilma); 14 RLG_famc9 (Daniela Danae Olivia); 15 RLC_famc2 (Barbara); 16 DTC_famc1 (Caspar Clifford Donald Heyjude); 17 RLG_famc14 (Lila); 18 RLG_famc15 (Jeli); 19 RLG_famc8 (Cereba Quinta); 20 DTC_famc6 (TAT1). c k-mer-defined proportion of repeats of the subgenomes. Cumulative genome coverage of 20- and 60-mers at increasing frequencies. Around 40% of each subgenome assembly consists of 20-mers occurring > = 100 times. At the 60-mer level the D subgenome has the highest and B the lowest proportion of repeats. d Distribution of 20-mer frequencies across physical chromosomes. The B subgenome has the lowest overall proportion of repeats