Implicit Transpositions in Shortest DCJ Scenarios

Jiang, Shuai; Alekseyev, Max A.

doi:10.1007/978-3-319-21233-3_2

Cited by 2 publications

(1 citation statement)

References 14 publications

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“…Some preliminary results of the present work appeared in the proceedings of the 2nd International Conference on Algorithms for Computational Biology (Jiang and Alekseyev, 2015 ).…”

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confidence: 95%

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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“…Some preliminary results of the present work appeared in the proceedings of the 2nd International Conference on Algorithms for Computational Biology (Jiang and Alekseyev, 2015 ).…”

mentioning

confidence: 95%

Implicit Transpositions in DCJ Scenarios

2017

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Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

Hartmann

Middendorf

Bernt

2017

Methods in Molecular Biology

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Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.

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Implicit Transpositions in Shortest DCJ Scenarios

Cited by 2 publications

References 14 publications

Implicit Transpositions in DCJ Scenarios

Implicit Transpositions in DCJ Scenarios

Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

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