Principle of the classification of breakpoints. Classification of breakpoints is exemplified by real data. Chromosomes for each species are drawn as colored boxes, with chromosome numbers indicated in the boxes. Positions along the genome (base pairs or cM) are written on the right. Breaks in boxes and * indicate evolutionary breakpoints. Genomes are drawn aligned along the human and mouse sequences. a) The breakpoint occurs solely in the bovine genome, in both genome alignments. This situation is classified as a BTA breakpoint. b) The breakpoint involves two mouse chromosome segments based on the human alignment. When aligned on the mouse genome, these segments define breakpoints in both human and bovine genomes. This situation is classified as a MMU breakpoint. c) The breakpoint involves both the bovine and the mouse genomes based on the human alignment. When aligned along the mouse genome, these regions define breakpoints only in the human genome. This situation is classified as a HSA breakpoint. d) The breakpoint involves either telomeres or centromeres. This situation is classified as TeloCentro. e) The breakpoint is classified in a different way according to the human and mouse alignments. This situation is classified as a breakpoint Reuse.