Evolutionary Distance in the Yeast Genome

Authors: Somayyeh Azizi, Saeed Kaboli, Atsushi Yagi

Abstract:

Whole genome duplication (WGD) increased the number of yeast Saccharomyces cerevisiae chromosomes from 8 to 16. In spite of retention the number of chromosomes in the genome of this organism after WGD to date, chromosomal rearrangement events have caused an evolutionary distance between current genome and its ancestor. Studies under evolutionary-based approaches on eukaryotic genomes have shown that the rearrangement distance is an approximable problem. In the case of S. cerevisiae, we describe that rearrangement distance is accessible by using dedoubled adjacency graph drawn for 55 large paired chromosomal regions originated from WGD. Then, we provide a program extracted from a C program database to draw a dedoubled genome adjacency graph for S. cerevisiae. From a bioinformatical perspective, using the duplicated blocks of current genome in S. cerevisiae, we infer that genomic organization of eukaryotes has the potential to provide valuable detailed information about their ancestrygenome.

Keywords: Whole-genome duplication, Evolution, Double-cutand- join operation, Yeast.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1330503

References:

[1] Wolfe KH, Shields DC, "Molecular evidence for an ancient duplication of the entire yeast genome", Nature 387, 708┬▒713, 1997.
[2] Seoighe C, Wolfe KH, "Updated map of duplicated regions in the yeast genome", Gene 238, 253-261, 1999.
[3] Kellis M, Birren BW, Lander ES, "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae", Nature 428: 617-624, 2004.
[4] Vitkup D, Kharchenko P, Wagner A, "Influence of metabolic network structure and function on enzyme evolution", Genome Biol 7: R39,2006.
[5] Conant GC, Wolfe KH, "Turning a hobby into a job: how duplicated genes find new functions", Nat Rev Genet 9: 938-950, 2008.
[6] Gordon JL, Byrne KP, Wolfe KH, "Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome", Plos Genet 5(5) e1000485, 2009.
[7] Gordon JL, Byrne KP, Wolfe KH, "Mechanisms of chromosome number evolution in yeast", Plos Genet 7(7) e1002190, 2011.
[8] Christie, D.A., "Sorting by block-interchanges", Inf. Process. Lett. 60, 165-169, 1996.
[9] Yacopoulos S, Attie O, Friedberg R, "Efficient sorting of genomic permutations by translocation, inversion and block interchange", Bioinformatics 21(16): 3340-3346, 2005.
[10] Kahn CL, Mozes S, Raphael B J, "Efficient algorithms for analyzing segmental duplications with deletions and inversion in genomes", Algorithms for Molecular Biology 5: 11, 2010.
[11] Thomas A, Varré JS, Ouangraoua A, "Genome dedoubling by DCJ and reversal", BMC bioinformatics 12(Suppl 9):S20, 2011.
[12] Chen X, Sun R, Yu J, "Approximating the double-cut-and-join distance between unsigned genomes", BMC Bioinformatics 12 (Suppl 9): S17, 2011.
[13] Mewes HW, Albermann K, BaÉhr M, Frishman D, Gleissner A et al., "Overview of the yeast genome", Nature 387, Suppl., 7±65,1997.