A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes

Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) (Nomascus leucogenys leucogenys) as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon–human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution

Breakpoint Validation by FISH

<div><p>(A) FISH experiments to validate breakpoints identified by array painting. Images 1 and 2 show hybridization on NLE metaphase preparations with human BACs spanning breakpoints identified by array painting. The yellow color in image 1 is due to the overlap of red and green spots as both BACs map on the same chromosome. Image 3 shows a similar experiment done on HLA metaphase preparations. The reciprocal position of the BACs used in each experiment is shown in the boxes below the images.</p><p>(B) FISH validation experiments on six gibbon BAC clones spanning three reciprocal breakpoints for the same rearrangement. In the diagrams, the rearrangements are illustrated starting from the ancestral chromosome form. Abbreviation: AC, ancestral chromosome.</p><p>(C) Gibbon BACs spanning inversion breakpoints were tested by FISH on human and gibbon metaphases. A BAC spanning an inversion in gibbon is expected to give a split signal on the human chromosome and a single signal on the corresponding gibbon chromosome.</p></div

Comparative Map of Human and Gibbon Chromosomes

<p>Ideogram of human chromosomes with orthologous gibbon chromosomes identified by array painting represented by colored bars to the left of each chromosome. Each segment is named after the gibbon chromosome followed by a small letter that refers to its mapping order in the gibbon chromosome. The BOSRs have been defined for convenience by numbers (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020223#pgen-0020223-t001" target="_blank">Table 1</a>). Gibbon clones spanning breakpoints identified by BES mapping are also located on the map. Clones with map positions that disagree with the array-painting map are italicized.</p

Association of the Breakpoint Regions with Segmental Duplication

<div><p>(A) The figure shows the sampling distribution of the overlap between SDs and a random set of regions obtained by relocating our original sample 1,000 times in the corresponding chromosomes. The original sample fell more than three standard deviations away from the mean of the simulated distribution (red arrow).</p><p>(B) The regions from the original sample were expanded in 100 kb increments. The number of regions overlapping with SDs at each step is shown.</p><p>(C) We measured the amount of overlap (in base pairs) of our 100 regions, while shifting each of them up to 5 Mb left and right of their original positions in 100 kb increments. The strong correlation between the original position (red arrow) and SD content is shown.</p></div