Abstract
Background: Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organization into circular unichromosomal genomes (as in most prokaryotes) and linear multichromosomal genomes (as in most eukaryotes). Very few of these models support gene duplications and losses—yet these events may be more common in evolutionary history than rearrangements and themselves cause apparent rearrangements.
Results: We propose a new evolutionary model that integrates gene duplications and losses with genome rearrangements and that leads to genomes with either one (or a very few) circular chromosome or a collection of linear chromosomes. Moreover, our model predictions fit observations about the evolution of gene family sizes as well as existing predictions about the growth in the number of chromosomes in eukaryotic genomes. Finally, our model is based on the existing inversion/translocation models and inherits their linear-time algorithm for pairwise distance computation.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bader, D.A., Moret, B.M.E., Yan, M.: A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8(5), 483–491 (2001)
Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)
Bergeron, A., Mixtacki, J., Stoye, J.: A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theor. Computer Science 410(51), 5300–5316 (2009)
Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press, Cambridge (2009)
Hahn, M.W., De Bie, T., Stajich, J.E., Nguyen, C., Cristianini, N.: Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research 15(8), 1153–1160 (2005)
Hannenhalli, S., Pevzner, P.A.: Transforming mice into men (polynomial algorithm for genomic distance problems). In: Proc. 36th IEEE Symp. Foundations of Comput. Sci. (FOCS 1995), pp. 581–592. IEEE Computer Society Press, Piscataway (1995)
Huynen, M.A., van Nimwegen, E.: The frequency distribution of gene family sizes in complete genomes. Mol. Biol. Evol. 15(5), 583–589 (1998)
Imai, H.T.: On the origin of telocentric chromosomes in mammals. J. Theor. Biol. 71(4), 619–637 (1978)
Imai, H.T., Crozier, R.H.: Quantitative analysis of directionality in mammalian karyotype evolution. American Naturalist 116(4), 537–569 (1980)
Imai, H.T., Maruyama, T., Gojobori, T., Inoue, Y., Crozier, R.H.: Theoretical bases for karyotype evolution. 1. the minimum-interaction hypothesis. American Naturalist 128(6), 900–920 (1986)
Imai, H.T., Satta, Y., Wada, M., Takahata, N.: Estimation of the highest chromosome number of eukaryotes based on the minimum interaction theory. J. Theor. Biol. 217(1), 61–74 (2002)
Koonin, E.V., Wolf, Y.I., Karev, G.P.: The structure of the protein universe and genome evolution. Nature 420, 218–223 (2002)
Lin, Y., Moret, B.M.E.: Estimating true evolutionary distances under the dcj model. In: Proc. 16th Conf. Intelligent Systems for Mol. Biol. (ISMB 2008). Bioinformatics, vol. 24(13), pp. i114–i122 (2008)
Lin, Y., Rajan, V., Swenson, K.M., Moret, B.M.E.: Estimating true evolutionary distances under rearrangements, duplications, and losses. In: Proc. 8th Asia Pacific Bioinformatics Conf, APBC 2010 (accepted, to appear, 2010)
Luscombe, N.M., Qian, J., Zhang, Z., Johnson, T., Gerstein, M.: The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biology 3(8) (2002)
Lynch, M.: The Origins of Genome Architecture. Sinauer (2007)
Qian, J., Luscombe, N.M., Gerstein, M.: Protein family and fold occurrence in genomes: power-law behavior and evolutionary model. J. Mol. Biol. 313, 673–681 (2001)
Rokas, A., Holland, P.W.H.: Rare genomic changes as a tool for phylogenetics. Trends in Ecol. and Evol. 15, 454–459 (2000)
Sturtevant, A.H.: A case of rearrangement of genes in Drosophila. Proc. Nat’l Acad. Sci., USA 7, 235–237 (1921)
Sturtevant, A.H., Dobzhansky, T.: Inversions in the third chromosome of wild races of Drosophila pseudoobscura, and their use in the study of the history of the species. Proc. Nat’l Acad. Sci., USA 22, 448–450 (1936)
Volff, J.-N., Altenbuchner, J.: A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186, 143–150 (2000)
Yanai, I., Camacho, C.J., DeLisi, C.: Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys. Rev. Lett. 85(12), 2641–2644 (2000)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lin, Y., Moret, B.M.E. (2010). A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_19
Download citation
DOI: https://doi.org/10.1007/978-3-642-16181-0_19
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16180-3
Online ISBN: 978-3-642-16181-0
eBook Packages: Computer ScienceComputer Science (R0)