Combinatorial RNA Interference In Caenorhabditis elegans Reveals That Redundancy Between Gene Duplicates Can Be Maintained For More Than 80 Million Years of Evolution

Background: Systematic analyses of loss-of-function phenotypes have been carried out for mostgenes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although suchstudies vastly expand our knowledge of single gene function, they do not address redundancy ingenetic networks. Developing tools for the systematic mapping of genetic interactions is thus a keystep in exploring the relationship between genotype and phenotype.Results: We established conditions for RNA interference (RNAi) in C. elegans to target multiplegenes simultaneously in a high-throughput setting. Using this approach, we can detect the greatmajority of previously known synthetic genetic interactions. We used this assay to examine theredundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs inS. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundantfunctions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence ofC. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressureto maintain the overlap in function between some gene duplicates.Conclusion: We established a high throughput method for examining genetic interactions usingcombinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicatedgenes can retain redundant functions for more than 80 million years of evolution. This providesstrong support for evolutionary models that predict that genetic redundancy between duplicatedgenes can be actively maintained by natural selection and is not just a transient side effect of recentgene duplication events.