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Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

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Models and Algorithms for Genome Evolution

Part of the book series: Computational Biology ((COBO,volume 19))

Abstract

The evolution of genomes can be studied at least three different scales: the nucleotide level, accounting for substitutions and indels, the gene level, accounting for gains and losses, and the genome level, accounting for rearrangements of chromosome organization. While the nucleotide and gene levels are now often integrated in a single model using reconciled gene trees, very little work integrates the genome level as well, and considers gene trees and gene orders simultaneously. In a seminal book chapter published in 2000 and entitled “Duplication, Rearrangement and Reconciliation”, Sankoff and El-Mabrouk outlined a general approach, making a step in that direction. This avenue has been poorly exploited by the community for over ten years, but recent developments allow the design of integrated methods where phylogeny informs the study of synteny and vice versa. We review these developments and show how this influence of synteny on gene tree construction can be implemented.

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Acknowledgements

This work is funded by the Agence Nationale pour la Recherche, Ancestrome project ANR-10-BINF-01-01.

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Authors and Affiliations

  1. LaBRI, Université Bordeaux I, Talence, France

    Cedric Chauve

  2. Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada

    Cedric Chauve

  3. DIRO, Université de Montréal, Montréal, QC, Canada

    Nadia El-Mabrouk

  4. LBBE, Université Lyon I Claude Bernard, Lyon, France

    Laurent Guéguen, Magali Semeria & Eric Tannier

  5. INRIA, Rhône-Alpes, France

    Eric Tannier

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  1. Cedric Chauve
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  2. Nadia El-Mabrouk
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  3. Laurent Guéguen
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  4. Magali Semeria
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  5. Eric Tannier
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Correspondence to Cedric Chauve .

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Editors and Affiliations

  1. Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada

    Cedric Chauve

  2. Computer Science and Operations Research, University of Montreal, Montreal, Québec, Canada

    Nadia El-Mabrouk

  3. Biometry and Evolutionary Biology, INRIA Rhône-Alpes, University of Lyon, Villeurbanne, France

    Eric Tannier

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Chauve, C., El-Mabrouk, N., Guéguen, L., Semeria, M., Tannier, E. (2013). Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later. In: Chauve, C., El-Mabrouk, N., Tannier, E. (eds) Models and Algorithms for Genome Evolution. Computational Biology, vol 19. Springer, London. https://doi.org/10.1007/978-1-4471-5298-9_4

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