Gibbon Hi-C map highlights nonreference chromosomal rearrangements. (A, bottom) Whole-genome Hi-C interaction matrix is shown for the gibbon named Vok (photo shown on the right) aligned to the reference gibbon genome (Nleu3.0). (Top) A close-up view of the Hi-C data corresponding to the reciprocal translocation between gibbon Chromosomes 1 and 22 shows a lack of intra-chromosomal interactions in the regions mobilized by the rearrangement, and stronger-than-expected inter-chromosomal interactions. (B, top) A scheme demonstrates the reciprocal translocation that formed NLE1a/22a (present in Vok) from the ancestral NLE 1b/22b (present in reference). (Bottom) FISH validation of the rearrangement on Vok chromosomes with chromosome paints for NLE 1b (green) and NLE 22b (red). (C, top) Hi-C matrix for NLE 7b displays an example of “ghost interactions” between regions corresponding to human Chromosome 22 separated by a pericentromeric inversion of the ancestral NLE 7a. (Bottom) FISH with the chromosome paint for human Chr 22 (red) shows a split signal indicative of the inversion in Vok, but not the sister taxa Nomascus gabriellae. (Gibbon chromosomes are labeled outside of chromosome ideograms, and corresponding human chromosomes are color coded and indicated within ideograms.)