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Genome Biology and Evolution Advance Access published online on June 27, 2009
Genome Biology and Evolution, doi:10.1093/gbe/evp016
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Deletional Bias across the Three Domains of Life

Chih-Horng Kuo and Howard Ochman*

Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721

* Author for Correspondence: Howard Ochman, Department of Ecology & Evolutionary Biology, 233 Life Sciences South, 1007 E. Lowell St., University of Arizona, Tucson, Arizona 85721; 520-626-8355 (phone); 520-621-3709 (fax); hochman{at}email.arizona.edu


  Abstract

Elevated levels of genetic drift are hypothesized to be a dominant factor that influences genome size evolution across all life forms. However, increased levels of drift appear to be correlated with genome expansion in eukaryotes but with genome contraction in bacteria, suggesting that these two groups of organisms experience vastly different mutational inputs and selective constraints. To determine the contribution of small insertion and deletion events to the differences in genome organization between eukaryotes and prokaryotes, we systematically surveyed 17 taxonomic groups across the three domains of life. Based on over 5,000 indel events in non-coding regions, we found that deletional events outnumbered insertions in all groups examined. The extent of deletional bias, when measured by the total length of insertions to deletions, revealed a marked disparity between eukaryotes and prokaryotes; while the ratio was close to one in the three eukaryotic groups examined, deletions outweighed insertions by at least a factor of ten in most prokaryotes. Moreover, the strength of deletional bias is associated the proportion of coding regions in prokaryotic genomes. Considering that genetic drift is a stochastic process and does not discriminate the exact nature of mutations, the degree of bias toward deletions provides an explanation to the differential responses of eukaryotes and prokaryotes to elevated levels of drift. Furthermore, deletional bias, rather than natural selection, is the primary mechanism by which the compact gene packing within most prokaryotic genomes is maintained.

Keywords: genome evolution, genome size, mutational spectra, organismal complexity, indels

Received May 4, 2009; Revised June 17, 2009; Accepted June 20, 2009


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