Rapid divergence in expression between duplicate genes inferred from microarray data

For more than 30 years, expression divergence has been considered as a major reason for retaining duplicated genes in a genome, but how often and how fast duplicate genes diverge in expression has not been studied at the genomic level. Using yeast microarray data, we show that expression divergence between duplicate genes is significantly correlated with their synonymous divergence (K-S) and also with their nonsynonymous divergence (K-A) if K(A)less than or equal to0.3. Thus, expression divergence increases with evolutionary time, and K-A is initially coupled with expression divergence. More interestingly, a large proportion of duplicate genes have diverged quickly in expression and the vast majority of gene pairs eventually become divergent in expression. Indeed, more than 40% of gene pairs show expression divergence even when K-S isless than or equal to0.10, and this proportion becomes >80% for K-S > 1.5. Only a small fraction of ancient gene pairs do not show expression divergence.