Abstract
BackgroundWhile gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most duplicate genes preserve (or subdivide) the functions of the parental gene or acquire new functions. One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes.ResultsHere we build a human gene coexpression network using human tissue-specific microarray data and investigate the divergence of duplicate genes in it. The topology of this network is scale-free. Interestingly, our analysis indicates that duplicate genes rapidly lose shared coexpressed partners: after approximately 50 million years since duplication, the two duplicate genes in a pair have only slightly higher number of shared partners as compared with two random singletons. We also show that duplicate gene pairs quickly acquire new coexpressed partners: the average number of partners for a duplicate gene pair is significantly greater than that for a singleton (the latter number can be used as a proxy of the number of partners for a parental singleton gene before duplication). The divergence in gene expression between two duplicates in a pair occurs asymmetrically: one gene usually has more partners than the other one. The network is resilient to both random and degree-based in silico removal of either singletons or duplicate genes. In contrast, the network is especially vulnerable to the removal of highly connected genes when duplicate genes and singletons are considered together.ConclusionDuplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons.Contact: kdm16@psu.eduSupplementary information: Please see additional files.
Highlights
While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated
Do most duplicate genes retain the functions of their parental singleton gene? Or do they diverge after duplication? And how rapidly does this divergence occur? Several models predicting preservation of both duplicate gene copies have been proposed [5,6,7] and reviewed in [8,9], their relative prevalence in the fates of duplicate genes is presently unknown
Description of the network To build the gene coexpression network, we used the mRNA expression data that provide information about ~45,000 transcripts assayed in 79 human tissues [37]
Summary
While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. Several models predicting preservation of both duplicate gene copies (e.g., gene function conservation, subfunctionalization, neofunctionalization, and subneofunctionalization) have been proposed [5,6,7] and reviewed in [8,9], their relative prevalence in the fates of duplicate genes is presently unknown. These questions were addressed by analysis of the protein-coding sequences of duplicate genes. The availability of genome-wide mRNA expression data allows one to study another important aspect of duplicate gene evolution, that is divergence in gene expression after duplication (e.g., [12,13,14,15])
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