Abstract
Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double-Cut-and-Join (DCJ) operations represent a convenient model of most common genome rearrangements (reversals, translocations, fissions, and fusions), while other genome rearrangements, such as transpositions, can be modeled by pairs of DCJs. Since the DCJ model does not directly account for transpositions, their impact on DCJ scenarios is unclear. In the present work, we study implicit appearance of transpositions (as pairs of DCJs) in DCJ scenarios. We consider shortest DCJ scenarios satisfying the maximum parsimony assumption, as well as more general DCJ scenarios based on some realistic but less restrictive assumptions. In both cases, we derive a uniform lower bound for the rate of implicit transpositions, which depends only on the genomes but not a particular DCJ scenario between them. Our results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes. We estimate that for mammalian genomes implicit transpositions constitute at least 6% of genome rearrangements.
Highlights
Genome rearrangements are dramatic evolutionary events that change genome structures
We estimate the rate of implicit transpositions recovered from pairwise DCJ scenarios between mammalian genomes, and between yeast genomes
For each pair of genomes, we use Corollary 14 and Corollary 17 for proper and shortest DCJ scenarios, respectively, to compute the lower bound for the rate of disjoint implicit transpositions between these genomes
Summary
Genome rearrangements are dramatic evolutionary events that change genome structures. The most common rearrangements are reversals that inverse contiguous segments of chromosomes, translocations that exchange tails of two chromosomes, and fissions/fusions that split/merge chromosomes All these rearrangements can be conveniently modeled by DoubleCut-and-Join (DCJ) operations (Yancopoulos et al, 2005), known as 2-breaks (Alekseyev and Pevzner, 2008), which make up to 2 “cuts” in a genome and “glue” the resulting genomic fragments in a new order. We pose a question of how many transpositions can be simultaneously recovered from a given DCJ scenario by shuffling DCJs and replacing suitable pairs of consecutive DCJs with transpositions We consider both shortest DCJ scenarios resulting from the maximum parsimony assumption, and more general proper DCJ scenarios based on some realistic but less restrictive assumptions.
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