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The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes
Fares, Mario A Keane, Orla M Toft, Christina Carretero-Paulet, Lorenzo Jones, Gary W
Fares, Mario A
Keane, Orla M
Toft, Christina
Carretero-Paulet, Lorenzo
Jones, Gary W
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2013-01-03
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Fares MA, Keane OM, Toft C, Carretero-Paulet L, and Jones GW. 2013. The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes. PLoS Genetics 9 (1): e1003176. doi:10.1371/journal.pgen.1003176
Abstract
Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this
process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely
to be retained than small-scale duplications (SSDs), though their relative contribution to the functional fate of duplicates
remains unexplored. Using the map of genetic interactions and the re-sequencing of 27 Saccharomyces cerevisiae genomes
evolving for 2,200 generations we show that SSD-duplicates lead to neo-functionalization while WGD-duplicates partition
ancestral functions. This conclusion is supported by: (a) SSD-duplicates establish more genetic interactions than singletons
and WGD-duplicates; (b) SSD-duplicates copies share more interaction-partners than WGD-duplicates copies; (c) WGDduplicates
interaction partners are more functionally related than SSD-duplicates partners; (d) SSD-duplicates gene copies
are more functionally divergent from one another, while keeping more overlapping functions, and diverge in their subcellular
locations more than WGD-duplicates copies; and (e) SSD-duplicates complement their functions to a greater extent
than WGD–duplicates. We propose a novel model that uncovers the complexity of evolution after gene duplication