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

  • Cedric Chauve
  • Nadia El-Mabrouk
  • Laurent Guéguen
  • Magali Semeria
  • Eric Tannier
Part of the Computational Biology book series (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.

Notes

Acknowledgements

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

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Copyright information

© Springer-Verlag London 2013

Authors and Affiliations

  • Cedric Chauve
    • 1
    • 2
  • Nadia El-Mabrouk
    • 3
  • Laurent Guéguen
    • 4
  • Magali Semeria
    • 4
  • Eric Tannier
    • 4
    • 5
  1. 1.LaBRIUniversité Bordeaux ITalenceFrance
  2. 2.Department of MathematicsSimon Fraser UniversityBurnabyCanada
  3. 3.DIROUniversité de MontréalMontréalCanada
  4. 4.LBBEUniversité Lyon I Claude BernardLyonFrance
  5. 5.INRIARhône-AlpesFrance

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