Figure 2

Genomic rearrangements (Adapted from [2] and [5]). a1 and a2 Genomic rearrangements resulting from recombination between low-copy repeats (LCRs). LCRs are depicted as black arrows with the orientation indicated by the direction of the arrowhead. Capital letters above the thin horizontal lines refer to the flanking unique sequences (for example, A). Homologues on the other strand (can be another chromatid or the homologous chromosome) are also shown (for example, a). Thin diagonal lines refer to a recombination event with the results shown by numbers 1, 2 and 3. a1 Recombination between direct repeats results in deletion and/or duplication. a2 Recombination between inverted repeats results in an inversion. b. Schematic representation of reciprocal duplications and deletions mediated by interchromosomal (left), interchromatid (middle) and intrachromatid (right) non-allelic homologous recombination (NAHR) using LCR pairs in direct orientation. Chromosomes are shown in black, with the centromere depicted by hashed lines. Yellow arrows depict LCRs. Letters adjacent to the chromatids refer to the flanking unique sequence (for example, A, a). Interchromosomal and interchromatid NAHR between LCRs in direct orientation result in reciprocal duplication and deletion, whereas intrachromatid NAHR only creates deletion. Signatures of homologous recombination include the sequence identity of the substrates (LCRs) used for NAHR, recombination hotspots within the LCRs, and evidence for gene conversion at the crossovers within the LCRs.