Inversion variants in human and primate genomes

Abstract

For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies. We identified a total of 156 putative inversions, between 103 kb and 91 Mb, corresponding to 136 human loci. Combining literature, sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one or multiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated with human disease. This work doubles the number of validated primate inversions larger than 100 kb, beyond what was previously documented. We identified 74 sites of errors, where the sequence has been assembled in the wrong orientation, in the reference genomes analyzed. Our data serve two purposes: First, we generated a map of evolutionary inversions in these genomes representing a resource for interrogating differences among these species at a functional level; second, we provide a list of misassembled regions in these primate genomes, involving over 300 Mb of DNA and 1978 human genes. Accurately annotating these regions in the genome references has immediate applications for evolutionary and biomedical studies on primates.

Figure 1.

Inversions map of human Chromosome 7. (A) Ideograms for human Chromosome 7 (HSA7) and its chimpanzee (PTR7), gorilla (GGO7), orangutan (PAB7), and macaque (MMU3) homologs. Ideograms only show previously reported inversions larger than 5 Mb. Synteny blocks, distinguished by colors and numbers, represent regions that are inverted in at least one of the species analyzed, but the order of the markers within the block is conserved in all of the different species. Green arrows indicate inverted blocks with respect to human orientation. (B) UCSC Genome Browser view of Chromosome 7 net alignments and inversions predicted in this study between human and nonhuman primate genomes. Regions called to be inverted in this study are shown as green, red, and black horizontal bars and represent real, false, and not determined (ND) inversions, respectively. Synteny block colors are consistent with panel A and allow for comparison of regions called to be inverted in this study with previously identified inversions. For example, Chr7_inv1 corresponds to an inversion involving synteny blocks 2 (blue) and 3 (yellow) that was previously reported in orangutan and macaque (shown in panel A). (C) Circos diagram (Krzywinski et al. 2009) reporting all validated evolutionary inversions between human Chromosome 7 and its primate homologs.

Figure 2.

Experimental validation of Chr7_inv10 inversion. (A) UCSC Genome Browser view of Chr7_inv10 (hg38_panTro5_30), exclusively predicted in the chimpanzee lineage. BES pair mapping of primate clones and their Illumina sequencing (reads in the colored frames) show that all primates analyzed carry the inverted orientation. Discordant clones spanning the inversion breakpoints appear to be discontinuous due to the presence of the inversion. (B) The same inversion has been further validated by FISH in human (GM12878), chimpanzee (PTR8), gorilla (GGO2), orangutan (PPY9), and macaque (MMU2) individuals using the FISH clones shown in panel A.

Figure 3.

Map of primate inversions and assemblies errors. (A) All inversions discovered and validated between human, chimpanzee, gorilla, orangutan, and macaque chromosomes are shown on the left side of the chromosome ideograms. In particular, previously reported inversions reidentified in the current study are represented by colored blocks with a diagonal pattern, while novel inversions are depicted with solid color blocks. Errors in human and nonhuman primate assemblies are shown on the right side of the chromosome ideograms. (B) The horizontal bar chart shows the number of inversions per human chromosome. (C) Megabases (Mb) of assembly errors are shown for each species. (D) All inversions for which the lineage specificity has been determined are mapped on a phylogenetic tree (Sudmant et al. 2013) in which the branch thickness is proportional to the number of inversions. (HSA) Homo sapiens, (PTR) Pan troglodytes, (GGO) Gorilla gorilla, (PPY) Pongo pygmaeus, (MMU) Macaca mulatta.