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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References
Alekseyev, M.A., Pevzner, P.A.: Colored de bruijn graphs and the genome halving problem. IEEE/ACM TCBB 4(1), 98–107 (2007)
Applegate, D., Bixby, R., Chvatal, V., Cook, W.: Concorde TSP solver (2006), http://www.tsp.gatech.edu/concorde/
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)
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)
El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM Journal on Computing 32(1), 754–792 (2003)
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)
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)
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)
Lin, S., Kernighan, B.W.: An effective heuristic algorithm for the traveling salesman problem. Operations Research 21, 498–516 (1973)
Ma, J., et al.: Reconstructing contiguous regions of an ancestral genome. Genome Research 16, 1557–1565 (2007)
Ma, J., et al.: Dupcar: Reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology 15(8), 1–21 (2008)
Salse, J., et al.: Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. PNAS 106(35), 14908–14913 (2009)
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)
Zheng, C., Zhu, Q., Sankoff, D.: Descendants of whole genome duplication within gene order phylogeny. Journal of Computational Biology 15(8), 947–964 (2008)
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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. https://doi.org/10.1007/978-3-642-15294-8_7
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DOI: https://doi.org/10.1007/978-3-642-15294-8_7
Publisher Name: Springer, Berlin, Heidelberg
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