Abstract
In a comparative map, the number of translocations in the evolutionary history of a chromosome can be estimated solely on the basis of the conserved syntenies it contains. This estimate, subtracted from the number of conserved segments, then allows the estimation of the number of inversions that have affected the chromosome. Summing these estimates over all chromosomes provides a startlingly accurate estimator (as assessed by simulation) of the total number of rearrangements of each type occurring in the evolutionary divergence of two genomes.
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References
Bed’hom, B.: Evolution of karyotype organization in Accipitridae: A translocation model. In: Sankoff, D., Nadeau, J.H. (eds.) Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families, pp. 347–356. Kluwer, Dordrecht (2000)
Burt, D.W.: Origin and evolution of avian microchromosomes. Cytogenetic and Genome Research 96, 97–112 (2002)
De, A., Ferguson, M., Sindi, S., Durrett, R.: The equilibrium distributionfor a generalized Sankoff-Ferretti model accurately predicts chromosomesize distributions in a wide variety of species. Journal of Applied Probability 38, 324–334 (2001)
Hannenhalli, S., Pevzner, P.A.: Transforming men into mice (polynomialalgorithm for genomic distance problem). In: Proceedings of the IEEE 36th Annua lSymposium on Foundations of Computer Science, pp. 581–592 (1995)
Housworth, E.A., Postlethwait, J.: Measures of synteny conservation between species pairs. Genetics 162, 441–448 (2002)
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., Haussler, D.: Evolution’s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences, USA 100, 11484–11489 (2003)
Mefford, H.C., Trask, B.J.: The complex structure and dynamic evolution of human subtelomeres. Nature Reviews in Genetics 3, 91–102 (2002)
Nadeau, J.H., Taylor, B.A.: Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences, USA 81, 814–818 (1984)
Pevzner, P.A., Tesler, G.: Genome rearrangements in mammalian genomes: Lessons from human and mouse genomic sequences. Genome Research 13, 37–45 (2003)
Pevzner, P.A., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proceedings of the National Academy of Sciences, USA 100, 7672–7677 (2003)
Sankoff, D., Deneault, M., Turbis, P., Allen, C.P.: Chromosomal distributions of breakpoints in cancer, infertility and evolution. Theoretical Population Biology 61, 497–501 (2002)
Sankoff, D., Ferretti, V.: Karotype distributions in a stochastic model of reciprocal translocation. Genome Research 6, 1–9 (1996)
Sankoff, D., Ferretti, V., Nadeau, J.H.: Conserved segment identification. Journal of Computational Biology 4, 559–565 (1997)
Sankoff, D., Parent, M.-N., Bryant, D.: Accuracy and robustness of analyses based on numbers of genes in observed segments. In: Sankoff, D., Nadeau, J.H. (eds.) Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families, pp. 299–306. Kluwer, Dordrecht (2000)
Sankoff, D., Parent, M.-N., Marchand, I., Ferretti, V.: On the Nadeau- Taylor theory of conserved chromosome segments. In: Hein, J., Apostolico, A. (eds.) CPM 1997. LNCS, vol. 1264, pp. 262–274. Springer, Heidelberg (1997)
Sankoff, D., Nadeau, J.H.: Conserved synteny as a measure of genomic distance. Discrete Applied Mathematics 71, 247–257 (1996)
Sankoff, D., Trinh, P.: Chromosomal breakpoint re-use in the inference of genome sequence rearrangement. In: Proceedings of RECOMB 2004, Eighth International Conference on Computational Molecular Biology, pp. 30–35. ACM Press, New York (2004)
Schubert, I., Oud, J.L.: There is an upper limit of chromosome size for normal development of an organism. Cell 88, 515–520 (1997)
Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences 65, 587–609 (2002)
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Sankoff, D., Mazowita, M. (2005). Estimators of Translocations and Inversions in Comparative Maps. In: Lagergren, J. (eds) Comparative Genomics. RCG 2004. Lecture Notes in Computer Science(), vol 3388. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32290-0_9
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DOI: https://doi.org/10.1007/978-3-540-32290-0_9
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