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International Conference on Algorithms for Computational Biology

AlCoB 2015: Algorithms for Computational Biology pp 13–24Cite as

Implicit Transpositions in Shortest DCJ Scenarios

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9199))

Abstract

Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double-Cut-and-Join (DCJ) operations represent a convenient model of most common genome rearrangements (reversals, translocations, fissions, and fusions), while other genome rearrangements, such as transpositions, can be modeled by pairs of DCJs. Since the DCJ model does not directly account for transpositions, their impact on DCJ scenarios is unclear.

In the current work, we study implicit appearance of transpositions (as pairs of DCJs) in shortest DCJ scenarios and prove uniform lower and upper bounds for their proportion. Our results imply that implicit transpositions may be unavoidable and even appear in a significant proportion for some genomes. We estimate that in mammalian evolution transpositions constitute at least \(17\,\%\) of genome rearrangements.

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Notes

  1. 1.

    Shao el al. [14] studies more general trajectory graphs, from which the dependency graphs can be obtained by contraction of edges.

  2. 2.

    We remark that since the set of shared genes varies across genome pairs, the DCJ distances between genomes in different pairs are incomparable.

References

  1. Alekseyev, M.A.: Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes. J. Comput. Biol. 15(8), 1117–1131 (2008)

    Article  MathSciNet  Google Scholar 

  2. Alekseyev, M.A., Pevzner, P.A.: Multi-break rearrangements and chromosomal evolution. Theor. Comput. Sci. 395(2), 193–202 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  3. Alexeev, N., Aidagulov, R., Alekseyev, M.A.: A computational method for the rate estimation of evolutionary transpositions. In: Ortuño, F., Rojas, I. (eds.) IWBBIO 2015, Part I. LNCS, vol. 9043, pp. 471–480. Springer, Heidelberg (2015)

    Google Scholar 

  4. Bader, M., Ohlebusch, E.: Sorting by weighted reversals, transpositions, and inverted transpositions. J. Comput. Biol. 14(5), 615–636 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  5. Braga, M.D., Stoye, J.: The solution space of sorting by DCJ. J. Comput. Biol. 17(9), 1145–1165 (2010)

    Article  MathSciNet  Google Scholar 

  6. Eriksen, N.: \((1+\epsilon )\)-approximation of sorting by reversals and transpositions. In: Gascuel, O., Moret, B.M. (eds.) WABI 2001. LNCS, vol. 2149, pp. 227–237. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  7. Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press, Cambridge (2009)

    Book  MATH  Google Scholar 

  8. Jiang, S., Alekseyev, M.A.: Weighted genomic distance can hardly impose a bound on the proportion of transpositions. In: Bafna, V., Sahinalp, S.C. (eds.) RECOMB 2011. LNCS, vol. 6577, pp. 124–133. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  9. Jiang, S., Alekseyev, M.A.: Linearization of median genomes under DCJ. In: Brown, D., Morgenstern, B. (eds.) WABI 2014. LNCS, vol. 8701, pp. 97–106. Springer, Heidelberg (2014)

    Google Scholar 

  10. Kasprzyk, A.: BioMart: driving a paradigm change in biological data management. Database 2011, bar049 (2011)

    Google Scholar 

  11. Ouangraoua, A., Bergeron, A.: Combinatorial structure of genome rearrangements scenarios. J. Comput. Biol. 17(9), 1129–1144 (2010)

    Article  MathSciNet  Google Scholar 

  12. Ozery-Flato, M., Shamir, R.: Sorting by translocations via reversals theory. In: Bourque, G., El-Mabrouk, N. (eds.) RECOMB-CG 2006. LNCS (LNBI), vol. 4205, pp. 87–98. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  13. Ranz, J., González, J., Casals, F., Ruiz, A.: Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution 57(6), 1325–1335 (2003)

    Article  Google Scholar 

  14. Shao, M., Lin, Y., Moret, B.: Sorting genomes with rearrangements and segmental duplications through trajectory graphs. BMC Bioinform. 14(15), 1–8 (2013)

    Google Scholar 

  15. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)

    Article  Google Scholar 

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Acknowledgments

The work was supported by the National Science Foundation under the grant No. IIS-1462107.

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Authors and Affiliations

  1. George Washington University, Washington DC, USA

    Shuai Jiang & Max A. Alekseyev

Authors
  1. Shuai Jiang
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  2. Max A. Alekseyev
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Corresponding author

Correspondence to Max A. Alekseyev .

Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Adrian-Horia Dediu

  2. Faculty of Science, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    Francisco Hernández-Quiroz

  3. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  4. Institute for Research in Applied Mathematics and Systems – IIMAS, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    David A. Rosenblueth

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© 2015 Springer International Publishing Switzerland

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Jiang, S., Alekseyev, M.A. (2015). Implicit Transpositions in Shortest DCJ Scenarios. In: Dediu, AH., Hernández-Quiroz, F., Martín-Vide, C., Rosenblueth, D. (eds) Algorithms for Computational Biology. AlCoB 2015. Lecture Notes in Computer Science(), vol 9199. Springer, Cham. https://doi.org/10.1007/978-3-319-21233-3_2

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  • DOI: https://doi.org/10.1007/978-3-319-21233-3_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-21232-6

  • Online ISBN: 978-3-319-21233-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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