Higher order repeat structures are prevalent in diverse animals and plants. (a) Graphical representation of higher order repeat structure compared to simple monomer repeats. In the higher order repeat, two variants, A and B, form a single dimer repeat that is repeated in tandem. When plotting repeat monomer length by GC content by genomic fraction, two distinct peaks are seen for Sorghum bicolor. The second peak (2) is exactly double the length of the first peak (1). (b) Sequence alignment of repeat units from a single Sorghum bicolor Sanger read that exhibits a higher order repeat structure consisting of an AB dimer. The arrows point to SNPs unique for either the A or B repeat of the dimer. (c) Neighbor joining analysis showing grouping of A and B repeats from sequence alignment in B. Bootstrap numbers are shown. (d) Higher order repeat structures can lead to novel centromere repeats. In New World monkeys, the two halves of the 343-bp monomer are weakly related to each other and to the 171-bp repeat in Old World monkeys and apes.
Melters et al. Genome Biology 2013 14:R10 doi:10.1186/gb-2013-14-1-r10