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Genome Biology

, 8:R209

First Online: 04 October 2007Received: 12 June 2007Revised: 03 October 2007Accepted: 04 October 2007

Abstract

BackgroundGenes 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.

ResultsWe 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.

ConclusionGenes, 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.

AbbreviationsGOGene Ontology

IPIinferred from protein interaction

Kanon-synonymous substitution rate

Kssynonymous substitution rate

ORFopen reading frame

SSDsmall-scale duplicate

WGDwhole-genome duplicate.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2007-8-10-r209 contains supplementary material, which is available to authorized users.

Luke Hakes, John W Pinney contributed equally to this work.

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Author: Luke Hakes - John W Pinney - Simon C Lovell - Stephen G Oliver - David L Robertson

Source: https://link.springer.com/



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