Abstract
Several mammalian genomes will only be sequenced at a 2X coverage, resulting in the impossibility of assembling contigs into chromosomes. We introduce the problem of ordering the contigs of two partially assembled genomes so as to maximize the similarity (measured in terms of genome rearrangements) between the assembled genomes. We give a linear-time algorithm for the Block Ordering Problem (BOP): Given two signed permutations (genomes) that are been broken into blocks (contigs), order and orient each set of blocks, in such a way that the number of cycles in the breakpoint graph of the resulting permutations is maximized. We illustrate our algorithm on a set of 90 markers from the human and mouse chromosomes X and show how the size of the contigs and the rearrangement distance between the two genomes affects the accuracy of the predicted assemblies. The appendix and an implementation are available at www.mcb.mcgill.ca/~egaul/recomb2006.
Keywords
- Genome rearrangement
- gene order
- breakpoint graph
- genome assembly
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References
Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research 14(4), 507–516 (2004)
Ma, J., Zhang, L., Suh, B., Raney, B.J., Kent, W.J., Blanchette, M., Haussler, D., Miller, W.: Reconstructing contiguous regions of an ancestral genome. Genome Research (in press, 2006)
Murphy, W.J., Larkin, D.M., van der Wind, A.E., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S.N., Milan, D., Ostrander, E.A., Pape, G., Parker, H.G., Raudsepp, T., Rogatcheva, M.B., Schook, L.B., Skow, L.C., Welge, M., Womack, J.E., O’brien, S.J., Pevzner, P.A., Lewin, H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734), 613–617 (2005)
El-Mabrouk, N., Nadeau, J., Sankoff, D.: Genome halving. In: Farach-Colton, M. (ed.) CPM 1998. LNCS, vol. 1448, pp. 235–250. Springer, Heidelberg (1998)
Murphy, W.J., Bourque, G., Tesler, G., Pevzner, P., O’Brien, S.J.: Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics 1(1), 30–40 (2003)
Tang, J., Moret, B.M.E.: Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics 19 (Suppl. 1), 305–312 (2003)
Tesler, G.: GRIMM: genome rearrangements web server. Bioinformatics 18(3), 492–493 (2002)
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)
Froenicke, L., CaldŽs, M.G., Graphodatsky, A., MŸller, 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. 16(3), 306–310 (2006)
Peng, Q., Pevzner, P.A., Tesler, G.: The Fragile Breakage versus Random Breakage Models of Chromosome Evolution. PLoS Comput. Biol. 2(2), 14 (2006)
Sankoff, D., Trinh, P.: Chromosomal breakpoint reuse in genome sequence rearrangement. J. Comput. Biol. 12(6), 812–821 (2005)
Margulies, E.H., Vinson, J.P., Miller, W., Jaffe, D.B., Lindblad-Toh, K., Chang, J.L., Green, E.D., Lander, E.S., Mullikin, J.C., Clamp, M.: (NISC) Comparative Sequencing Program. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc. Natl. Acad. Sci. USA 102(13), 4795–4800 (2005)
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R.K., Gibbs, R.A., Kent, W.J., Miller, W., Haussler, D.: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15(8), 1034–1050 (2005)
Bourque, G., Pevzner, P.A.: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. 12(1), 26–36 (2002)
Bergeron, A.: A very elementary presentation of the Hannenhalli-Pevzner theory. Discrete Applied Mathematics 146(2), 134–145 (2005)
Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip polynomial algorithm for sorting signed permutations by reversals. In: Proceedings of the 27th Annual ACM Symposium on the Theory of Computing, pp. 178–187 (1995)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)
Zheng, C., Lenert, A., Sankoff, D.: Reversal distance for partially ordered genomes. Bioinformatics 21(suppl. 1), i502–i508 (2005)
Bergeron, A., Mixtacki, J., Stoye, J.: 10. In: Mathematics of Evolution and Phylogeny: the Inversion Distance Problem, 1st edn., pp. 262–290. Oxford University Press, Oxford (2005)
Pevzner, P., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. Natl. Acad. Sci. USA 100(13), 7672–7677 (2003)
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Gaul, É., Blanchette, M. (2006). Ordering Partially Assembled Genomes Using Gene Arrangements. In: Bourque, G., El-Mabrouk, N. (eds) Comparative Genomics. RCG 2006. Lecture Notes in Computer Science(), vol 4205. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11864127_10
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DOI: https://doi.org/10.1007/11864127_10
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-44529-6
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