Linearization of Median Genomes under DCJ

Jiang, Shuai; Alekseyev, Max A.

doi:10.1007/978-3-662-44753-6_8

Cited by 2 publications

(2 citation statements)

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“…Recently it was shown (Jiang and Alekseyev, 2014 ) that any shortest DCJ scenario between a genome with m ≥ 1 circular chromosomes and a linear genome (consisting of linear chromosomes) can be transformed this way into a shortest DCJ scenario, where circular chromosomes are eliminated by the first m DCJs and the rest represents a scenario between linear genomes. This construction was further used to obtain an approximate solution for the linear genome median problem.…”

Section: Discussionmentioning

confidence: 99%

“…In a DCJ scenario, one can change the order of two adjacent independent DCJs and obtain another DCJ scenario of the same length between the same two genomes. Similarly, a pair of adjacent weakly dependent DCJs in a DCJ scenario can be replaced with another pair of weakly dependent DCJs, resulting in a new DCJ scenario of the same length between the same two genomes (Braga and Stoye, 2010 ; Jiang and Alekseyev, 2014 ).…”

Section: Shuffling Of Dcj Scenarios and Dependency Graphsmentioning

confidence: 99%

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Implicit Transpositions in DCJ Scenarios

2017

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Shuffling Of Dcj Scenarios and Dependency Graphsmentioning

confidence: 99%