Fig. 4

Base-composition distribution and frequency of tri-nucleotide motifs at each of three representing transition types. a The [T] values at each transition type of C/T (top), G/T (middle), and A/T transition type (bottom) within bread wheat and its wild progenitors (including bread wheat variety (V), landrace-west (L-W), landrace-east (L-E), durum (D), wild emmer (W), and Ae. tauschii (A)). For each transition type, the violins of three subgenomes are plotted together and separated by dashed lines. For each plot, the length of black arrow presents the [T]-difference on corresponding transition type of A or B subgenome between bread wheat and wild emmer, whereas the length of red arrow presents the [T]-difference on corresponding transition type of D subgenome between bread wheat and Ae. tauschii. b Frequency of 48 motifs at C/T (top), G/T (middle), and A/T transition type (bottom). For each plot, blue, red, and green bars show A, B, and D subgenome, respectively. The numbers 1–16 on Y-axis show 16 motifs, 5′-ANA-3′, 5′-ANC-3′, 5′-ANG-3′, 5′-ANT-3′, 5′-CNA-3′, 5′-CNC-3′, 5′-CNG-3′, 5′-CNT-3′, 5′-GNA-3′, 5′-GNC-3′, 5′-GNG-3′, 5′-GNT-3′, 5′-TNA-3′, 5′-TNC-3′, 5′-TNG-3′, and 5′-TNT-3′ in order, where N is the corresponding transition type. The horizontal line in each plot indicated the expected frequency at 0.01 (≈ 1/96). The 17 motifs with frequency above the threshold are marked by arrows, including 5 motifs with frequency more than twice the threshold marked by red arrows. Correspondingly, the reverse and complementary 48 motifs around A/G, A/C, and C/G types are also provided in Fig. S13