Sorting genomes with centromeres by translocations

Michal Ozery-Flato, Ron Shamir

Research output: Contribution to journalArticlepeer-review

Abstract

A centromere is a special region in the chromosome that plays a vital role during cell division. Every new chromosome created by a genome rearrangement event must have a centromere in order to survive. This constraint has been ignored in the computational modeling and analysis of genome rearrangements to date. Unlike genes, the different centromeres are indistinguishable, they have no orientation, and only their location is known. A prevalent rearrangement event in the evolution of multi-chromosomal species is translocation (i.e., the exchange of tails between two chromosomes). A translocation may create a chromosome with no centromere in it. In this paper, we study for the first time centromeres-aware genome rearrangements. We present a polynomial time algorithm for computing a shortest sequence of translocations transforming one genome into the other, where all of the intermediate chromosomes must contain centromeres. We view this as a first step towards analysis of more general genome rearrangement models that take centromeres into consideration.

Original languageEnglish
Pages (from-to)793-812
Number of pages20
JournalJournal of Computational Biology
Volume15
Issue number7
DOIs
StatePublished - 1 Sep 2008

Keywords

  • Combinatorics
  • Comparative genomics
  • Genome rearrangements
  • Sorting by translocations

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