Nucleotide diversity in the wheat genome. (A) The average number of SNPs per kilobase between the three wheat types Chinese Spring (C), Opata (O) and W7984 (W) is shown across all three subgenomes (ABD) or in the individual subgenomes (A, B and D). The numbers on the outside of the triangles gives the diversity across all sequences in the respective subgenomes, those on the inside give the diversity in coding sequences only. (B) Diversity between homeologous genes. Full-length cDNAs  were aligned to our assembly of W7984 and assigned to one of the subgenomes using the genetic anchoring of the assembly. This plot shows the distribution of nucleotide identity between cDNAs assigned to the A, B and D subgenomes and their best BLAST hit in the other two subgenomes (that is, to their putative homeologous loci).