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