%0 Journal Article
%T Novel genes exhibit distinct patterns of function acquisition and network integration
%A John A Capra
%A Katherine S Pollard
%A Mona Singh
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-12-r127
%X We examine the function and evolution of new genes in the yeast Saccharomyces cerevisiae. We observed significant differences in the functional attributes and interactions of genes created at different times and by different mechanisms. Novel genes are initially less integrated into cellular networks than duplicate genes, but they appear to gain functions and interactions more quickly than duplicates. Recently created duplicated genes show evidence of adapting existing functions to environmental changes, while young novel genes do not exhibit enrichment for any particular functions. Finally, we found a significant preference for genes to interact with other genes of similar age and origin.Our results suggest a strong relationship between how and when genes are created and the roles they play in the cell. Overall, genes tend to become more integrated into the functional networks of the cell with time, but the dynamics of this process differ significantly between duplicate and novel genes.Large-scale genome sequencing efforts have made it increasingly possible to study the genetics of species divergence on a genome-wide scale. Comparing the complete genomes of many closely related species in the context of well-resolved phylogenetic trees provides clues about the genomic events and evolutionary processes that generate functionally-relevant differences between species. Several studies have identified lineage-specific differences in the gene sets of recently diverged species in many clades [1-4], and these observed differences often contribute to functional divergence between species [5-7]. Understanding the origin and function of new genes is critically important to deciphering the evolution of cellular networks and genomes; however, previous analyses have not taken into account the different evolutionary mechanisms that can produce new genes.New genes are created by a variety of processes, including gene duplication, domain shuffling, incorporation of mobile elements,
%U http://genomebiology.com/2010/11/12/R127