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Evolutionary Genomics pp 397–429Cite as

Analysis of Gene Order Evolution Beyond Single-Copy Genes

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 855))

Abstract

The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics, based on the representation of genomes as ordered sequences of signed genes. We specifically focus on the “hard part” of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy, and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss, and speciation), the cluster level (evolution by tandem duplications), and the genome level (all types of rearrangement events, including whole genome duplication).

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Authors and Affiliations

  1. Département d’Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC, Canada

    Nadia El-Mabrouk

  2. Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada

    David Sankoff

Authors
  1. Nadia El-Mabrouk
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  2. David Sankoff
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Correspondence to David Sankoff .

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  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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El-Mabrouk, N., Sankoff, D. (2012). Analysis of Gene Order Evolution Beyond Single-Copy Genes. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 855. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-582-4_15

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  • DOI: https://doi.org/10.1007/978-1-61779-582-4_15

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