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Reconstructing the History of Syntenies Through Super-Reconciliation

  • Mattéo Delabre
  • Nadia El-MabroukEmail author
  • Katharina T. Huber
  • Manuel Lafond
  • Vincent Moulton
  • Emmanuel Noutahi
  • Miguel Sautie Castellanos
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11183)

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.

Keywords

Gene tree Reconciliation Duplication Loss Synteny 

Supplementary material

473852_1_En_10_MOESM1_ESM.pdf (2.6 mb)
Supplementary material 1 (pdf 2690 KB)

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Mattéo Delabre
    • 1
  • Nadia El-Mabrouk
    • 1
    Email author
  • Katharina T. Huber
    • 2
  • Manuel Lafond
    • 3
  • Vincent Moulton
    • 2
  • Emmanuel Noutahi
    • 1
  • Miguel Sautie Castellanos
    • 1
  1. 1.Département d’informatique (DIRO)Université de MontréalMontréalCanada
  2. 2.School of Computing SciencesUniversity of East AngliaNorwichUK
  3. 3.Department of Computer ScienceUniversité de SherbrookeSherbrookeCanada

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