We are analyzing https://link.springer.com/article/10.1186/gb-2006-7-8-r69.

Title:
Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution | Genome Biology
Description:
Background Systematic analyses of loss-of-function phenotypes have been carried out for most genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although such studies vastly expand our knowledge of single gene function, they do not address redundancy in genetic networks. Developing tools for the systematic mapping of genetic interactions is thus a key step in exploring the relationship between genotype and phenotype. Results We established conditions for RNA interference (RNAi) in C. elegans to target multiple genes simultaneously in a high-throughput setting. Using this approach, we can detect the great majority of previously known synthetic genetic interactions. We used this assay to examine the redundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs in S. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundant functions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence of C. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressure to maintain the overlap in function between some gene duplicates. Conclusion We established a high throughput method for examining genetic interactions using combinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicated genes can retain redundant functions for more than 80 million years of evolution. This provides strong support for evolutionary models that predict that genetic redundancy between duplicated genes can be actively maintained by natural selection and is not just a transient side effect of recent gene duplication events.
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Keywords {🔍}

genes, rnai, gene, elegans, phenotypes, pubmed, duplicated, combinatorial, article, redundant, genetic, google, scholar, phenotype, interactions, synthetic, data, redundancy, single, pairs, cas, functions, genome, size, duplicates, table, file, duplicate, dilution, caenorhabditis, additional, analysis, wildtype, targeting, central, figure, embryonic, worms, found, rrf, evolution, cerevisiae, brood, orthologs, bacterial, yeast, essential, function, lossoffunction, briggsae,

Topics {✒️}

article download pdf article number r69 combinatorial rna-mediated interference isopropyl-beta-d-thiogalactopyranoside rna-expressing bacteria leads rna-expressing bacterial clones 'wild-type brood size' diluting dsrna-expressing strain rnai-hypersensitive rrf-3 background position-specific gap penalties dsrna-expressing bacterial strain transient gene knock-downs unrelated dsrna-expressing bacteria rrf-3 rnai-hypersensitive strain full size image false-negative rates induced combinatorial rna interference score post-embryonic phenotypes rna-mediated interference ras-induced vulval development duplicate brood size nontargeting dsrna-expressing bacteria post-embryonic genetic interactions explore genetic interactions 'wild-type embryonic survival' enhanced rna interference full access diverse signaling pathways brood size defect privacy choices/manage cookies authors’ original file brood size defects genetic interaction networks koonin ev bacterial strain expressing genome-wide rnai analysis synthetic lethal pair apparent redundant functions additional data files partially redundant functions larval growth arrest liquid feeding assay synthetic phenotypic effects combinatorial rnai targets wild-type brood transient state resulting caenorhabditis elegans reveals caenorhabditis elegans ortholog generating additive phenotypes dsrna-expressing bacteria

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         headline:Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution
         description:Systematic analyses of loss-of-function phenotypes have been carried out for most genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although such studies vastly expand our knowledge of single gene function, they do not address redundancy in genetic networks. Developing tools for the systematic mapping of genetic interactions is thus a key step in exploring the relationship between genotype and phenotype. We established conditions for RNA interference (RNAi) in C. elegans to target multiple genes simultaneously in a high-throughput setting. Using this approach, we can detect the great majority of previously known synthetic genetic interactions. We used this assay to examine the redundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs in S. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundant functions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence of C. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressure to maintain the overlap in function between some gene duplicates. We established a high throughput method for examining genetic interactions using combinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicated genes can retain redundant functions for more than 80 million years of evolution. This provides strong support for evolutionary models that predict that genetic redundancy between duplicated genes can be actively maintained by natural selection and is not just a transient side effect of recent gene duplication events.
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         Brood Size
         Redundant Function
         Duplicate Gene Pair
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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            address:
               name:CRG-EMBL Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
               type:PostalAddress
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      affiliation:
            name:Simon Fraser University
            address:
               name:Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
               type:PostalAddress
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      affiliation:
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