Sorting Signed Permutations by Inverse Tandem Duplication Random Losses

IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov-Dec;18(6):2177-2188. doi: 10.1109/TCBB.2019.2917198. Epub 2021 Dec 8.

Abstract

Gene order evolution of unichromosomal genomes, for example mitochondrial genomes, has been modelled mostly by four major types of genome rearrangements: inversions, transpositions, inverse transpositions, and tandem duplication random losses. Generalizing models that include all those rearrangements while admitting computational tractability are rare. In this paper, we study such a rearrangement model, namely the inverse tandem duplication random loss (iTDRL) model, where an iTDRL duplicates and inverts a continuous segment of a gene order followed by the random loss of one of the redundant copies of each gene. The iTDRL rearrangement has currently been proposed by several authors suggesting it to be a possible mechanisms of mitochondrial gene order evolution. We initiate the algorithmic study of this new model of genome rearrangement by proving that a shortest rearrangement scenario that transforms one given gene order into another given gene order can be obtained in quasilinear time. Furthermore, we show that the length of such a scenario, i.e., the minimum number of iTDRLs in the transformation, can be computed in linear time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Evolution, Molecular
  • Gene Duplication / genetics*
  • Gene Order / genetics
  • Gene Rearrangement / genetics*
  • Genome, Mitochondrial / genetics
  • Genomics
  • Models, Genetic*