Implicit Transpositions in Shortest DCJ Scenarios
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.
KeywordsGenome rearrangements Transpositions DCJ
The work was supported by the National Science Foundation under the grant No. IIS-1462107.
- 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
- 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
- 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