The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Abstract

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements.

Results: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA.

Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

Figure 1

Distribution of SDs identities relative to major rearrangements (Inversions) between humans and chimpanzees. In Blue, the distribution of percentages of SDs that are located within the inversion of human chromosomes rearranged relative to chimpanzees. In pink, the distribution of SDs in rearranged chromosomes but outside the rearrangements. In green the percentages of identities of SDs located in chromosomes that are collinear (not rearranged) for both species.

Figure 2

Distribution of identities relative to major rearrangements between human and chimpanzees for individual chromosomes. Chromosomes without any pair of copies of SDs within rearrangements are not shown (see Methods).

Figure 3

Distribution of SDs identities relative to simulated pericentromeric rearrangements in colinear chromosomes between humans and chimpanzees.

Figure 4

Distribution of SDs identities relative to simulated pericentric rearrangements in colinear chromosomes between humans and chimpanzees for individual chromosome. Chromosomes without any pair of copies of SDs within simulated rearrangements are not shown (see Methods).