Sequence, structural and expression divergence of duplicate genes in the bovine genome.

Xiaoping Liao,Yan Meng,Graham Plastow,Paul Stothard,Hua Bao,Stephen Moore,William Barendse

doi:10.1371/journal.pone.0102868

Abstract

Gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. In the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. A total of 3131 putative duplicated gene pairs were identified, including 712 cattle-specific duplicate gene pairs unevenly distributed across the genome, which are significantly enriched for specific biological functions including immunity, growth, digestion, reproduction, embryonic development, inflammatory response, and defense response to bacterium. Around 97.1% (87.8%) of (cattle-specific) duplicate gene pairs were found to have distinct exon-intron structures. Analysis of gene expression by RNA-Seq and sequence divergence (synonymous or non-synonymous) revealed that expression divergence is correlated with sequence divergence, as has been previously observed in other species. This analysis also led to the identification of a subset of cattle-specific duplicate gene pairs exhibiting very high expression divergence. Interestingly, further investigation revealed a significant relationship between structural and expression divergence while controlling for the effect of synonymous sequence divergence. Together these results provide further insight into duplicate gene sequence and expression divergence in cattle, and their potential contributions to phenotypic divergence.

Highlights

Gene duplication is thought to be a major driving force of evolution as it provides raw materials that selection can act upon [1,2,3]
We investigated the relationship between structural and expression divergence and found that expression divergence was on average greater for duplicate gene pairs exhibiting exon-intron structure divergence, regardless of their overall level of synonymous sequence divergence, suggesting structural divergence may be partially responsible for the divergent expression pattern observed
We examined whether the proportion of duplicate gene pairs with different exon-intron structure is correlated with evolutionary time

Summary

Introduction

Gene duplication is thought to be a major driving force of evolution as it provides raw materials that selection can act upon [1,2,3]. Several previous studies have investigated divergence between duplicate genes at the genome scale [7,8,9,10,11,12,13,14,15,16]. In Arabidopsis, over 95% of duplicate genes studied have diverged in exon-intron structure, and structural divergence occurs largely proportionally to evolutionary time [7]. Gu et al examined expression divergence between 400 duplicate gene pairs in yeast using microarray data and found a positive correlation between synonymous sequence divergence (a proxy of evolutionary time) and expression divergence [10]. A later study in Arabidopsis found that synonymous sequence divergence and expression divergence were not correlated [14]

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