MBE Advance Access published online on September 3, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm183
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Research Article |
The Role of Mutational Dynamics in Genome Shrinkage.
Theoretical Biology/Bioinformatics Group, Utrecht University, Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
1 Author to whom correspondence should be addressed. E-mail: M.J.A.vanHoek{at}bio.uu.nl; Tel: +31 30 2531497; Fax: +31 30 2513655
Received for publication February 26, 2007. Revision received August 13, 2007. Accepted for publication August 22, 2007.
Genome shrinkage occurs after whole genome duplications and in the evolution of parasitic or symbiotic species. The dynamics of this process, whether it occurs by single gene deletions, or also by larger deletions are however unknown. In yeast, genome shrinkage has occurred after a whole genome duplication. Using a computational model of genome evolution we show that in a random genome single gene deletions cannot explain the observed pattern of gene loss in yeast. The distribution of genes deleted per event can be very well described by a geometric distribution, with a mean of 1.1 genes per event. In terms of deletions of a stretch of base pairs, we find that a geometric distribution with an average of 500-600 base pairs per event describes the data very well. Moreover, in the model, as in the data, gene pairs which have a small intergenic distance are more likely to be both deleted. This proves that simultaneous deletion of multiple genes causes the observed pattern of gene deletions, rather than deletion of functionally clustered genes by selection. Furthermore, we found that in the bacterium Buchnera aphidicola larger deletions than in yeast are necessary to explain the clustering of deleted genes. We show that the excess clustering of deleted genes in B. aphidicola can be explained by the clustering of genes in operons. Therefore we show that selection has little effect on the clustering of deleted genes after the WGD in yeast, while it has during genome shrinkage in B. aphidicola.
Key Words: whole genome duplication • genome shrinkage • Saccharomyces cerevisiae • Buchnera aphidicola • gene deletion • computational model