The evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplication

dc.contributor.authorDefoort, Jonas
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorCarretero-Paulet, Lorenzo
dc.date.accessioned2020-01-31T05:11:31Z
dc.date.available2020-01-31T05:11:31Z
dc.date.issued2019-08
dc.description.abstractGene duplicates, generated through either whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechanism of origin, a behavior that is hypothesized to stem from constraints to maintain the relative dosage balance between the genes concerned and their interaction context. However, the mechanisms ultimately influencing loss and retention of gene duplicates over evolutionary time are not yet fully elucidated. Here, by using a robust classification of gene duplicates in Arabidopsis thaliana, Solanum lycopersicum, and Zea mays, large RNAseq expression compendia and an extensive protein–protein interaction (PPI) network from Arabidopsis, we investigated the impact of PPIs on the differential evolutionary and functional fate of WGD and SSD duplicates. In all three species, retained WGD duplicates show stronger constraints to diverge at the sequence and expression level than SSD ones, a pattern that is also observed for shared PPI partners between Arabidopsis duplicates. PPIs are preferentially distributed among WGD duplicates and specific functional categories. Furthermore, duplicates with PPIs tend to be under stronger constraints to evolve than their counterparts without PPIs regardless of their mechanism of origin. Our results support dosage balance constraint as a specific property of genes involved in biological interactions, including physical PPIs, and suggest that additional factors may be differently influencing the evolution of genes following duplication, depending on the species, time, and mechanism of origin.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.librarianam2020en_ZA
dc.description.sponsorshipThe European Union Seventh Framework Program (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739.en_ZA
dc.description.urihttps://academic.oup.com/gbeen_ZA
dc.identifier.citationDefoort, J., Van de Peer, Y. & Carretero-Paulet, L. 2019, 'The evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplication', Genome Biology and Evolution, vol. 11, no. 8, pp. 2292-2305.en_ZA
dc.identifier.issn1759-6653 (online)
dc.identifier.other10.1093/gbe/evz156
dc.identifier.urihttp://hdl.handle.net/2263/73041
dc.language.isoenen_ZA
dc.publisherOxford University Pressen_ZA
dc.rights© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. TThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).en_ZA
dc.subjectExpression divergenceen_ZA
dc.subjectDuplicate retentionen_ZA
dc.subjectAngiospermsen_ZA
dc.subjectWhole genome duplication (WGD)en_ZA
dc.subjectSmall-scale duplication (SSD)en_ZA
dc.subjectProtein–protein interaction (PPI)en_ZA
dc.titleThe evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplicationen_ZA
dc.typeArticleen_ZA

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