Fig 1.
Experimental validation of genomic inversions at 15q25.
(A) UCSC Genome Browser view of the 15q25 region. Segmental duplication blocks A, B and C are shown with colored boxes. GOLGA repeat locations from blat analyses of GOLGA2P10 and GOLGA6L5P are depicted with green and red boxes mapping on the plus or minus strand, respectively. Proximal and distal tested inversions are shown with black arrows and fosmid clones used for FISH experiments on interphase nuclei are indicated with colored blocks followed by the fosmid names. Segmental duplication colors show the ancestral origins of duplications based on comparison with mammalian groups assigned by DupMasker [76]. (B) FISH results on interphase nuclei for proximal and distal inversions in each analyzed species. The color order indicates probes relative orientation, with red-green-blue signals showing haplotypes in direct orientation and green-red-blue signals showing inverted haplotypes. FISH analyses of the proximal inversion show that macaque, orangutan, and chimpanzee are all inverted when compared to the human reference genome orientation, while all gorillas are in direct orientation. The distal inversion is polymorphic within the chimpanzee population, while all the other species are inverted in the homozygous state when compared to human. Timing of species divergences is also shown at the top (mya = million years ago). HSA = Homo sapiens; PTR = Pan troglodytes; GGO = Gorilla gorilla; PPY = Pongo pygmaeus; MMU = Macaca mulatta.
Fig 2.
Strand-seq of the proximal inversion at 15q25.
On the left, ideograms of expected Strand-seq results for each possible inversion genotype are shown. On the right, a UCSC Genome Browser view (coordinates lifted to GRCh37/hg19) of Strand-seq data, BED-formatted and uploaded as custom tracks, of the three libraries is shown. For each cell, aligned reads are indicated as individual lines in Crick (teal) or Watson (orange) state. In the library on the top (HsSs_0256) mixed Watson and Crick reads at the proximal inversion (black arrow) indicate the heterozygosity of the region while in the others a direct orientation of the region is shown.
Table 1.
Summary of inversion frequencies in human and nonhuman primates.
Inversion frequencies for the proximal and distal region based on FISH, Strand-seq and optical mapping analyses are shown. The number of individuals tested for each species is shown in parenthesis.
Fig 3.
Bionano analysis of the 15q25 region.
Bionano optical mapping data of three great ape genomes at the 15q25 locus. The two black arrows in each plot denote the two loci where inversions are observed between the apes and human. Segmental duplication blocks A, B and C are also shown with colored boxes. In each display, the top and bottom maps represent the two alleles of the de novo assembled genomes for each species with respect to the human reference assembly (hg38 track). The individual labels represent the positions of the label motifs of the enzyme used. The top panel shows the alignments of the assembled Nt.BssSI genome maps of a chimpanzee sample. The blue labels are the aligned labels, whereas the yellow ones are unaligned labels. The middle panel shows gorilla maps generated by DLE-1 enzyme, and the blue and red labels represent aligned and unaligned labels, respectively. Finally, the bottom panel illustrates how an orangutan genome—constructed using Nb.BspQI—is aligned to human, with blue representing aligned labels and yellow the unaligned ones.
Fig 4.
Deletions at the 15q25 region.
Three different classes of microdeletions with breakpoints between segmental duplication blocks A-B, A-C and B-C are shown as colored boxes. Segmental duplications are shown with colored boxes. GOLGA repeat locations from the blat analysis of GOLGA2P10 and GOLGA6L5P are depicted with green and red boxes mapping on plus or minus strand, respectively. SNP array and whole-genome sequencing (WGS) data of a patient with a 15q25 A-B deletion are shown. The SNP array highlights a copy number (CN) of 2 for the parents while the proband shows a CN of 1 for the deleted region. WGS shows a CN of 2 for the regions flanking the microdeletion (black line) and a CN of 1 (red line) for the deleted region. At the bottom of the figure are shown the results of a blast2Seq alignment between the two microdeletion breakpoint intervals. The two largest alignments of 9.4 kbp (blast2SeqA) and 9 kbp (blast2SeqB) with 99% similarity are shown with light blue and yellow arrows, respectively. GOLGA2P10 repeats, which encompass the regions of high similarity at the breakpoints, are also shown in the zoom inset.
Fig 5.
Human chromosome 15 evolution and GOLGA core elements dispersion.
A fission event of an ancestral chromosome led to human and great ape chromosomes 14 (green ideogram) and 15 (blue ideogram). The zoomed-in view shows how the inactivation of the ancestral centromere after the fission event released the recombination constraints typical of pericentromeric regions leading to two inversions, shown with the white arrows, which resulted in a dispersal of GOLGA repeats (purple blocks) and segmental duplications (gray bars). AC, ancestral centromere. NC, neocentromere.