A Uniform Theory of Adequate Subgraphs for the Genome Median, Halving, and Aliquoting Problems
One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of pre-duplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole genome multiplication events leads to the genome aliquoting problem.
In the present study, we generalize the adequate subgraphs approach previously proposed for the genome median problem to the genome halving and aliquoting problems. Our study lays a theoretical foundation for practical algorithms for the reconstruction of pre-duplicated ancestral genomes.
KeywordsGenome rearrangement Breakpoint graph Adequate subgraph Whole genome duplication Genome halving Genome aliquoting Genome median
The work of Maria Atamanova was supported by the Government of the Russian Federation (Grant 08-08) and JetBrains Research.
- 1.Alekseyev, M.A., Pevzner, P.A.: Whole genome duplications, multi-break rearrangements, and genome halving problem. In: Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), pp. 665–679. Society for Industrial and Applied Mathematics, Philadelphia (2007)Google Scholar
- 4.Alexeev, N., Avdeyev, P., Alekseyev, M.A.: Comparative genomics meets topology: a novel view on genome median and halving problems. BMC Bioinform. 17(Suppl. 14), 213–223 (2016)Google Scholar
- 5.Avdeyev, P., Alexeev, N., Rong, Y., Alekseyev, M.A.: A unified ILP framework for genome median, halving, and aliquoting problems under DCJ. In: Meidanis, J., Nakhleh, L. (eds.) (RECOMB-CG). LNCS, vol. 10562, pp. 156–178. Springer, Heidelberg (2017). https://doi.org/10.1007/978-3-319-67979-2_9CrossRefGoogle Scholar
- 10.Gao, N., Yang, N., Tang, J.: Ancestral genome inference using a genetic algorithm approach. PLOS ONE 8(5), 1–6 (2013)Google Scholar
- 11.Gavranović, H., Tannier, E.: Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of saccharomyces cerevisiae. Pac. Symp. Biocomput. 15, 21–30 (2010)Google Scholar
- 23.Zhang, M., Arndt, W., Tang, J.: An exact solver for the DCJ median problem. In: Pacific Symposium on Biocomputing 2009, pp. 138–149. World Scientific (2009)Google Scholar