Analysis of segmental duplications reveals a distinct pattern of continuation-of-synteny between human and mouse genomes

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

Background

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals raised some doubts about their existence.

Results

Here we demonstrate that fragile regions are subject to a birth and death process, implying that fragility has a limited evolutionary lifespan.

Conclusions

This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions as a phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome.

Breakpoint graphs and ancestral genome reconstructions

Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.

Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion of transpositions. We further use these results to analyze comparative genomic architecture of mammalian genomes.

Are there rearrangement hotspots in the human genome?

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal of RBM caused a controversy and led to a split among researchers studying genome evolution. In particular, it remains unclear whether some complex rearrangements (e.g., transpositions) can create an appearance of rearrangement hotspots. We contribute to the ongoing debate by analyzing multi-break rearrangements that break a genome into multiple fragments and further glue them together in a new order. In particular, we demonstrate that (1) even if transpositions were a dominant force in mammalian evolution, the arguments in favor of FBM still stand, and (2) the "gene deletion" argument against FBM is flawed.