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Rapid divergence in expression between duplicate genes inferred from microarray data.

Zhenglong Gu1, Dan Nicolae, Henry H-S Lu

  • 1Dept of Ecology and Evolution, University of Chicago, 1101 East 57th Street, 60637, Chicago, IL, USA.

Trends in Genetics : TIG
|November 26, 2002
PubMed
Summary
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Gene duplication is often retained due to expression divergence. This study shows gene expression divergence increases with evolutionary time and most duplicate genes eventually diverge, even early in evolution.

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Gene duplication is a key driver of evolutionary innovation.
  • Expression divergence is hypothesized to be a major factor in retaining duplicated genes.
  • Previous studies lacked a genomic-level understanding of the rate and frequency of expression divergence.

Purpose of the Study:

  • To investigate the rate and frequency of expression divergence in duplicate genes at a genomic scale.
  • To determine the relationship between expression divergence and evolutionary time (synonymous and nonsynonymous divergence).

Main Methods:

  • Analysis of yeast microarray data.
  • Correlation analysis between expression divergence and synonymous divergence (K(S)).
  • Correlation analysis between expression divergence and nonsynonymous divergence (K(A)).

Related Experiment Videos

Main Results:

  • Expression divergence is significantly correlated with synonymous divergence (K(S)).
  • Expression divergence is correlated with nonsynonymous divergence (K(A)) for K(A) <= 0.3.
  • A substantial proportion of duplicate genes exhibit rapid expression divergence, with over 40% showing divergence even at low K(S) (<= 0.10).
  • The vast majority of gene pairs eventually become expression divergent (>80% for K(S) > 1.5).

Conclusions:

  • Expression divergence increases with evolutionary time.
  • Nonsynonymous divergence is initially coupled with expression divergence.
  • Most duplicate genes rapidly diverge in expression, contributing to their retention in the genome.
  • A small fraction of ancient gene pairs maintain similar expression patterns.