Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss
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).
KeywordsInternal Node Yeast Species Whole Genome Duplication Ancestral Genome Travel Salesperson Problem
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- 2.Applegate, D., Bixby, R., Chvatal, V., Cook, W.: Concorde TSP solver (2006), http://www.tsp.gatech.edu/concorde/
- 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.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
- 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.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
- 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