Research

All duplicates are not equal: the difference between small-scale and genome duplication

Luke Hakes^* , John W Pinney^* , Simon C Lovell , Stephen G Oliver and David L Robertson

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R209doi:10.1186/gb-2007-8-10-r209

Published:	4 October 2007

Subject areas: Bioinformatics, Evolution, Genome studies

Abstract

Background

Genes in populations are in constant flux, being gained through duplication and occasionally retained or, more frequently, lost from the genome. In this study we compare pairs of identifiable gene duplicates generated by small-scale (predominantly single-gene) duplications with those created by a large-scale gene duplication event (whole-genome duplication) in the yeast Saccharomyces cerevisiae.

Results

We find a number of quantifiable differences between these data sets. Whole-genome duplicates tend to exhibit less profound phenotypic effects when deleted, are functionally less divergent, and are associated with a different set of functions than their small-scale duplicate counterparts. At first sight, either of these latter two features could provide a plausible mechanism by which the difference in dispensability might arise. However, we uncover no evidence suggesting that this is the case. We find that the difference in dispensability observed between the two duplicate types is limited to gene products found within protein complexes, and probably results from differences in the relative strength of the evolutionary pressures present following each type of duplication event.

Conclusion

Genes, and the proteins they specify, originating from small-scale and whole-genome duplication events differ in quantifiable ways. We infer that this is not due to their association with different functional categories; rather, it is a direct result of biases in gene retention.