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Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

ABSTRACT: When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pairs in the Caenorhabditis elegans genome. Remarkably, in contrast to expectations, we find that phenotype masking makes only a minor contribution to the low knockdown phenotype rate for duplicate genes. Instead, we find that non-essential genes are highly over-represented among duplicates, leading to a low observed loss-of-function phenotype rate. We further find that duplicate pairs derived from essential and non-essential genes have contrasting evolutionary dynamics: whereas non-essential genes are both more often successfully duplicated (fixed) and lost, essential genes are less often duplicated but upon successful duplication are maintained over longer periods. We expect the fundamental evolutionary duplication dynamics presented here to be broadly applicable.

SUBMITTER: Woods S

PROVIDER: S-EPMC3649981 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

Woods Shane S Coghlan Avril A Rivers David D Warnecke Tobias T Jeffries Sean J SJ Kwon Taejoon T Rogers Anthony A Hurst Laurence D LD Ahringer Julie J

PLoS genetics 20130509 5

When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pair ...[more]

PMID: 23675306

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Dataset Information

Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

Publications

Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

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