Sequence architecture at synteny breaks of chromosome 9–14 translation between cattle (UMD3.1) and goat (CHIR_1.0). Panel A: A breakpoint region on CHI14 (10.40 Mb-11.08 Mb) mapping to two cattle centromeres. Panel B: A breakpoint on BTA9 (13.03 Mb-13.16 Mb) mapping to two goat centromeres. In each panel, [α] Goat-cattle DNA pairwise alignments are highlighted using colored curve; Self-comparisons of goat regions or cattle regions are grey. Each two neighboring synteny blocks are distinguished between in red curves with in green curves, respectively. Colors have not any biological meanings. [β] Segmental duplications longer than 3 kb are highlighted in grey (>5 kb are in red). Long segmental duplications are highly enriched in breakpoints comparing to synteny blocks. [γ] LINEs (green), SINEs (purple), Simple repeats (blue), and LTRs (yellow). [δ] Genes with colors denotes transcriptional orientation (the white represents “+” and the black represent “-“). [ϵ] Names of ANKRD26 homologsare marked in red. Breakpoint intervals were highlighted using mixture colored regions from two neighboring synteny blocks between cattle and goat, which revealed mosaic new insertions at rearrangement sites. Self-comparisons showed that these two centromeres share larger homologous region in cattle (panel A), different from in goat (panel B) suggest two cattle centromeres underwent a much longer evolution process than two goat centromeres. The breakpoint in goat genome (panel A) presents more complex architecture than one in cattle genome (panel B). Segmental duplications are enriched in breakpoints comparing to synteny blocks suggested that in these cases duplications promoted nonallelic homologous recombination (NAHR), and thus a chromosome rearrangement.