Abstract
Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral genomes of ciliate Paramecium tetraurelia.
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References
Caprara, A.: Formulations and hardness of multiple sorting by reversals. RECOMB, 84–94 (1999)
Pe’er, I., Shamir, R.: The median problems for breakpoints are NP-complete. Electronic Colloquium on Computational Complexity (ECCC), 5(71) (1998)
Sankoff, D., Blanchette, M.: Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5(3), 555–570 (1998)
Moret, B.M.E., Wyman, S.K., Bader, D.A., Warnow, T., Yan, M.: A new implmentation and detailed study of breakpoint analysis. PSB, 583–594 (2001)
Bourque, G., Pevzner, P.A.: Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12(1), 26–36 (2002)
Froenicke, L., Caldes, M.G., Graphodatsky, A., Muller, S., Lyons, L.A., Robinson, T.J., Volleth, M., Yang, F., Wienberg, J.: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res. Genome Res. 16(3), 306–310 (2006)
Bourque, G., Tesler, G., Pevzner, P.A.: The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 16(3), 311–313 (2006)
Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, W.J., Blanchette, M., Haussler, D., Miller, W.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16(12), 1557–1565 (2006)
Fitch, W.M.: Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416 (1971)
Rocchi, M., Archidiacono, N., Stanyon, R.: Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed. Genome Res. 16(12), 1441–1444 (2006)
Eichler, E.E., Sankoff, D.: Structural dynamics of eukaryotic chromosome evolution. Science 301(5634), 793–797 (2003)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Sankoff, D., El-Mabrouk, N.: Duplication, rearrangement and reconciliation. In: Sankoff, D., Nadeau, J.H. (eds.) Comparative genomics: Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families, pp. 537–550. Kluwer Academic Publishers, Dordrecht (2000)
Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic distances under deletions and insertions. Theor. Comput. Sci. 325(3), 347–360 (2004)
Page, R.D.M., Charleston, M.A.: From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7(2), 231–240 (1997)
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from Globin Sequences. Syst. Zool. 28(2), 132–163 (1979)
Guigo, R., Muchnik, I., Smith, T.F.: Reconstruction of ancient molecular phylogeny. Mol. Phylogenet. Evol. 6(2), 189–213 (1996)
Boesch, F.T., Gimpel, J.F.: Covering points of a digraph with point-disjoint paths and its application to code optimization. J. ACM. 24(2), 192–198 (1977)
Aury, J.M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B.M., Ségurens, B., Daubin, V., Anthouard, V., Aiach, N., et al.: Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444, 171–178 (2006)
Seoighe, C., Wolfe, K.H.: Extent of genomic rearrangement after genome duplication in yeast. PNAS 95(8), 4447–4452 (1998)
El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM J. Comput. 32(3), 754–792 (2003)
Alekseyev, M.A., Pevzner, P.A.: Whole genome duplications and contracted breakpoint graphs. SIAM J. Comput. 36(6), 1748–1763 (2007)
Zheng, C., Zhu, Q., Sankoff, D.: Genome halving with an outgroup. Evolutionary Bioinformatics 2, 319–326 (2006)
Chen, K., Durand, D., Farach-Colton, M.: NOTUNG: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7(3-4), 429–447 (2000)
Bansal, M.S., Burleigh, J.G., Eulenstein, O., Wehe, A.: Heuristics for the gene-duplication problem: A Θ(n) speed-up for the local search. RECOMB, pp. 238–252 (2007)
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Ma, J., Ratan, A., Zhang, L., Miller, W., Haussler, D. (2007). A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. In: Tesler, G., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2007. Lecture Notes in Computer Science(), vol 4751. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74960-8_10
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DOI: https://doi.org/10.1007/978-3-540-74960-8_10
Publisher Name: Springer, Berlin, Heidelberg
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