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Updated: Feb 15, 2026

Watershed Planning within a Quantitative Scenario Analysis Framework
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Implicit Transpositions in DCJ Scenarios.

Pavel Avdeyev1, Shuai Jiang2, Max A Alekseyev1

  • 1Department of Mathematics and the Computational Biology Institute, George Washington University, Washington, DC, United States.

Frontiers in Genetics
|January 10, 2018
PubMed
Summary
This summary is machine-generated.

Genome rearrangements, like transpositions, can be implicitly modeled by Double-Cut-and-Join (DCJ) operations. This study reveals that implicit transpositions are often unavoidable in DCJ scenarios, especially in mammalian genomes.

Keywords:
DCJbreakpoint graphschromosome evolutiongenome rearrangementstranspositions

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genome rearrangements are key drivers of genomic evolution, altering genome structure.
  • The Double-Cut-and-Join (DCJ) model is widely used to quantify evolutionary distance via genome rearrangements.
  • The DCJ model's handling of transpositions, a common rearrangement type, remains unclear.

Purpose of the Study:

  • To investigate the implicit occurrence of transpositions within Double-Cut-and-Join (DCJ) scenarios.
  • To establish a lower bound for the rate of implicit transpositions in DCJ analyses.
  • To assess the significance of implicit transpositions in comparative genomics.

Main Methods:

  • Analyzing shortest DCJ scenarios under maximum parsimony.
  • Examining more general DCJ scenarios with relaxed assumptions.
  • Deriving a uniform lower bound for implicit transposition rates based on genomic characteristics.

Main Results:

  • A uniform lower bound for implicit transposition rates was derived, independent of specific DCJ scenarios.
  • Implicit transpositions can be unavoidable or frequent depending on the genomes compared.
  • An estimation suggests implicit transpositions account for at least 6% of rearrangements in mammalian genomes.

Conclusions:

  • The DCJ model may implicitly encompass transpositions, impacting evolutionary distance calculations.
  • Understanding implicit transpositions is crucial for accurate phylogenomic analyses.
  • This work highlights the pervasive nature of transpositions in genome evolution, even when not explicitly modeled.