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

PLoS One. 2014 Jul 23;9(7):e102868. doi: 10.1371/journal.pone.0102868. eCollection 2014.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cattle / genetics*
  • Chromosomes, Mammalian / genetics
  • Gene Duplication
  • Gene Expression Profiling*
  • Genes, Duplicate / genetics*
  • Genetic Variation*
  • Genome / genetics*

Grants and funding

The study was made possible by funding provided by Genome Canada, Genome Alberta, Government of Alberta, Alberta Innovates BioSolutions, and the Alberta Livestock and Meat Agency. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.