Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

  • Denis Bertrand
  • Yves Gagnon
  • Mathieu Blanchette
  • Nadia El-Mabrouk
Conference paper

DOI: 10.1007/978-3-642-15294-8_7

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)
Cite this paper as:
Bertrand D., Gagnon Y., Blanchette M., El-Mabrouk N. (2010) Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. In: Moulton V., Singh M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science, vol 6293. Springer, Berlin, Heidelberg

Abstract

Whole genome duplication (WGD) is a rare evolutionary event that has played a dramatic role in the diversification of most eukaryotic lineages. Given a set of species known to have evolved from a common ancestor through one or many rounds of WGD together with a set of genome rearrangements, and a phylogenetic tree for these species, the goal is to infer the pre-duplication ancestral genomes. We use a two step approach: (1) Compute a score for each possible ancestral adjacency at each internal node of the phylogeny; (2) Combine adjacencies to form ancestral chromosomes. We first apply our method on simulated datasets and show a high accuracy for adjacency prediction. We then infer the pre-duplicated ancestor of a set of 11 yeast species and compare it to a manually assembled ancestral genome obtained by Gordon et al. (2009).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Denis Bertrand
    • 1
  • Yves Gagnon
    • 1
  • Mathieu Blanchette
    • 2
  • Nadia El-Mabrouk
    • 1
  1. 1.DIRO, Université de MontréalCanada
  2. 2.McGill Centre for BioinformaticsMcGill UniversityCanada

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