Algorithms in Bioinformatics

Volume 6293 of the series Lecture Notes in Computer Science pp 78-89

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

  • Denis BertrandAffiliated withDIRO, Université de Montréal
  • , Yves GagnonAffiliated withDIRO, Université de Montréal
  • , Mathieu BlanchetteAffiliated withMcGill Centre for Bioinformatics, McGill University
  • , Nadia El-MabroukAffiliated withDIRO, Université de Montréal

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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).