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

  • Denis Bertrand
  • Yves Gagnon
  • Mathieu Blanchette
  • Nadia El-Mabrouk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)


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).


Internal Node Yeast Species Whole Genome Duplication Ancestral Genome Travel Salesperson Problem 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Alekseyev, M.A., Pevzner, P.A.: Colored de bruijn graphs and the genome halving problem. IEEE/ACM TCBB 4(1), 98–107 (2007)PubMedGoogle Scholar
  2. 2.
    Applegate, D., Bixby, R., Chvatal, V., Cook, W.: Concorde TSP solver (2006),
  3. 3.
    Chauve, C., Gavranović, H., Ouangraoua, A., Tannier, E.: Yeast ancestral genome reconstructions: the possibilities of computational methods II. Journal of Computational Biology (2010) (in press)Google Scholar
  4. 4.
    Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. Plos Computational Biology 4(11), e1000234 (2008)Google Scholar
  5. 5.
    El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM Journal on Computing 32(1), 754–792 (2003)CrossRefGoogle Scholar
  6. 6.
    Gavranović, H., Tannier, E.: Guided genome halving: probably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. In: Pacific Symposium on Biocomputing, vol. 15, pp. 21–30 (2010)Google Scholar
  7. 7.
    Gordon, J.L., Byrne, K.P., Wolfe, K.H.: Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern saccharomyces cerevisiae genome. PloS Genetics 5(5), e1000485 (2009)Google Scholar
  8. 8.
    Hedtke, S.M., Townsend, T.M., Hillis, D.M.: Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55, 522–529 (2006)CrossRefPubMedGoogle Scholar
  9. 9.
    Lin, S., Kernighan, B.W.: An effective heuristic algorithm for the traveling salesman problem. Operations Research 21, 498–516 (1973)CrossRefGoogle Scholar
  10. 10.
    Ma, J., et al.: Reconstructing contiguous regions of an ancestral genome. Genome Research 16, 1557–1565 (2007)CrossRefGoogle Scholar
  11. 11.
    Ma, J., et al.: Dupcar: Reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology 15(8), 1–21 (2008)CrossRefGoogle Scholar
  12. 12.
    Salse, J., et al.: Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. PNAS 106(35), 14908–14913 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Zheng, C., Zhu, Q., Adam, Z., Sankoff, D.: Guided genome halving: hardness, heuristics and the history of the hemiascomycetes. In: ISMB, pp. 96–104 (2008)Google Scholar
  14. 14.
    Zheng, C., Zhu, Q., Sankoff, D.: Descendants of whole genome duplication within gene order phylogeny. Journal of Computational Biology 15(8), 947–964 (2008)CrossRefPubMedGoogle Scholar

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

Personalised recommendations