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Reconstructing the History of Syntenies Through Super-Reconciliation

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Comparative Genomics (RECOMB-CG 2018)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11183))

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Abstract

Classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is clearly not suited for genes grouped in syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation model, that extends the traditional Duplication-Loss model to the reconciliation of a set of trees, accounting for segmental duplications and losses. From a complexity point of view, we show that the associated decision problem is NP-hard. We then give an exact exponential-time algorithm for this problem, assess its time efficiency on simulated datasets, and give a proof of concept on the opioid receptor genes.

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Notes

  1. 1.

    The program and simulations are available at:

    https://github.com/UdeM-LBIT/SuperReconciliation.

  2. 2.

    https://useast.ensembl.org/index.html.

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Author information

Authors and Affiliations

  1. Département d’informatique (DIRO), Université de Montréal, Montréal, Québec, Canada

    Mattéo Delabre, Nadia El-Mabrouk, Emmanuel Noutahi & Miguel Sautie Castellanos

  2. School of Computing Sciences, University of East Anglia, Norwich, UK

    Katharina T. Huber & Vincent Moulton

  3. Department of Computer Science, Université de Sherbrooke, Sherbrooke, Canada

    Manuel Lafond

Authors
  1. Mattéo Delabre
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  2. Nadia El-Mabrouk
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  3. Katharina T. Huber
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  4. Manuel Lafond
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  5. Vincent Moulton
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  6. Emmanuel Noutahi
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  7. Miguel Sautie Castellanos
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Corresponding author

Correspondence to Nadia El-Mabrouk .

Editor information

Editors and Affiliations

  1. McGill University, Montréal, QC, Canada

    Mathieu Blanchette

  2. Université de Sherbrooke, Sherbrooke, QC, Canada

    Aïda Ouangraoua

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Delabre, M. et al. (2018). Reconstructing the History of Syntenies Through Super-Reconciliation. In: Blanchette, M., Ouangraoua, A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science(), vol 11183. Springer, Cham. https://doi.org/10.1007/978-3-030-00834-5_10

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  • DOI: https://doi.org/10.1007/978-3-030-00834-5_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-00833-8

  • Online ISBN: 978-3-030-00834-5

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