Abstract
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a single ancestral genome, use a scaffolding approach to select a subset of ancestral gene adjacencies. In this paper, we describe an exact algorithm for the small parsimony problem that combines both approaches. We consider that gene adjacencies at internal nodes of the species phylogeny are weighted, and we introduce an objective function defined as a convex combination of these weights and the evolutionary cost under the Single-Cut-or-Join (SCJ) model. We propose a Fixed-Parameter Tractable algorithm based on the Sankoff-Rousseau dynamic programming algorithm, that also allows to sample co-optimal solutions. An implementation is available at http://github.com/nluhmann/PhySca.
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References
Alekseyev, M., Pevzner, P.A.: Breakpoint graphs and ancestral genome reconstructions. Genome Res. 19, 943–957 (2009)
Bérard, S., Gallien, C., et al.: Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics 28, 382–388 (2012)
Bertrand, D., Gagnon, Y., Blanchette, M., El-Mabrouk, N.: Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss. In: Moulton, V., Singh, M. (eds.) WABI 2010. LNCS, vol. 6293, pp. 78–89. Springer, Heidelberg (2010)
Bos, K.I., Schuenemann, V., et al.: A draft genome of yersinia pestis from victims of the black death. Nature 478, 506–510 (2011)
Boža, V., Brejová, B., Vinař, T.: GAML: genome assembly by maximum likelihood. Algorithms Mol. Biol. 10, 18 (2015)
Chauve, C., Ponty, Y., Zanetti, J.: Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinform. 16(Suppl. 19), S6 (2015)
Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4, e1000234 (2008)
Denoeud, F., Carretero-Paulet, L., et al.: The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 125527 (2013)
Feijǎo, P., Meidanis, J.: SCJ: a breakpoint-like distance that simplifies several rearrangement problems. IEEE/ACM TCBB 8, 1318–1329 (2011)
Fitch, W.: Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Biol. 20, 406–416 (1971)
Kováč, J., Brejová, B., Vinař, T.: A practical algorithm for ancestral rearrangement reconstruction. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS, vol. 6833, pp. 163–174. springer, Heidelberg (2011)
Luhmann, N., Chauve, C., Stoye, J., Wittler, R.: Scaffolding of ancient contigs and ancestral reconstruction in a phylogenetic framework. In: Campos, S. (ed.) BSB 2014. LNCS, vol. 8826, pp. 135–143. Springer, Heidelberg (2014)
Luhmann, N., Thevenin, A., et al.: The SCJ small parsimony problem for weighted gene adjacencies (extended version) (2016). Preprint http://arxiv.org/abs/1603.08819
Ma, J., Zhang, L., et al.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16, 1557–1565 (2006)
Maňuch, J., Patterson, M., et al.: Linearization of ancestral multichromosomal genomes. BMC Bioinform. 13(Suppl. 19), S11 (2012)
Miklós, I., Smith, H.: Sampling and counting genome rearrangement scenarios. BMC Bioinform. 16(Suppl 14), S6 (2015)
Ming, R., Van Buren, R., et al.: The pineapple genome and the evolution of CAM photosynthesis. Nature Genet. 47, 1435 (2015)
Neafsey, D.E., Waterhouse, R.M., et al.: Highly evolvable malaria vectors: the genome of 16 Anopheles mosquitoes. Science 347, 1258522 (2015)
Rajaraman, A., Tannier, E., Chauve, C.: FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics 29, 2987–2994 (2013)
Sankoff, D., Rousseau, P.: Locating the vertices of a steiner tree in an arbitrary metric space. Math. Program. 9, 240–246 (1975)
Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10(1), 120 (2009)
Xu, A.W., Moret, B.M.E.: GASTS: parsimony scoring under rearrangements. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS, vol. 6833, pp. 351–363. Springer, Heidelberg (2011)
Zheng, C., Sankoff, D.: On the pathgroups approach to rapid small phylogeny. BMC Bioinform. 12(Suppl. 1), S4 (2011)
Acknowledgements
NL and RW are funded by the International DFG Research Training Group GRK 1906/1. CC is funded by NSERC grant RGPIN-249834.
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Luhmann, N., Thévenin, A., Ouangraoua, A., Wittler, R., Chauve, C. (2016). The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_17
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DOI: https://doi.org/10.1007/978-3-319-38782-6_17
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