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Permanent link (DOI): https://doi.org/10.7939/R3D795F3R

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

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Author or creator
Liao, X.
Bao, H.
Meng, Y.
Plastow, G.
Moore, S.
Stothard, P.
Additional contributors
Subject/Keyword
evolutionary genetics
genomic databases
immune response
sequence databases
gene expression
evolutionary immunology
sequence alignment
cattle
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
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.
Date created
2014
DOI
doi:10.7939/R3D795F3R
License information
Attribution 4.0 International
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Citation for previous publication
Liao, X., Bao, H., Meng, Y., Plastow, G., Moore, S., Stothard, P. (2014). Sequence, structural and expression divergence of duplicate genes in the bovine genome. PLoS One, 9(7), e102868.  http://dx.doi.org/10.1371/journal.pone.0102868

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