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

(2019) GENOME BIOLOGY AND EVOLUTION. 11(8). p.2292-2305
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Abstract
Gene 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 mechanism 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, Solanumlycopersicum, 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 ofWGD 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.
Keywords
WHOLE-GENOME DUPLICATION, PHYLOGENETIC ANALYSIS, PLANT COEXPRESSION, AGE, DISTRIBUTIONS, DOSAGE, POLYPLOIDY, EXPRESSION, DIVERGENCE, SELECTION, TANDEM, protein-protein interaction, expression divergence, whole genome, duplication, small-scale duplication, duplicate retention, angiosperms

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MLA
Defoort, Jonas, et al. “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, 2019, pp. 2292–305, doi:10.1093/gbe/evz156.
APA
Defoort, 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, 11(8), 2292–2305. https://doi.org/10.1093/gbe/evz156
Chicago author-date
Defoort, Jonas, Yves Van de Peer, and Lorenzo Carretero-Paulet. 2019. “The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication.” GENOME BIOLOGY AND EVOLUTION 11 (8): 2292–2305. https://doi.org/10.1093/gbe/evz156.
Chicago author-date (all authors)
Defoort, Jonas, Yves Van de Peer, and Lorenzo Carretero-Paulet. 2019. “The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication.” GENOME BIOLOGY AND EVOLUTION 11 (8): 2292–2305. doi:10.1093/gbe/evz156.
Vancouver
1.
Defoort J, Van de Peer Y, Carretero-Paulet L. The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication. GENOME BIOLOGY AND EVOLUTION. 2019;11(8):2292–305.
IEEE
[1]
J. Defoort, Y. Van de Peer, and L. Carretero-Paulet, “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, 2019.
@article{8629677,
  abstract     = {{Gene 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 mechanism 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, Solanumlycopersicum, 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 ofWGD 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.}},
  author       = {{Defoort, Jonas and Van de Peer, Yves and Carretero-Paulet, Lorenzo}},
  issn         = {{1759-6653}},
  journal      = {{GENOME BIOLOGY AND EVOLUTION}},
  keywords     = {{WHOLE-GENOME DUPLICATION,PHYLOGENETIC ANALYSIS,PLANT COEXPRESSION,AGE,DISTRIBUTIONS,DOSAGE,POLYPLOIDY,EXPRESSION,DIVERGENCE,SELECTION,TANDEM,protein-protein interaction,expression divergence,whole genome,duplication,small-scale duplication,duplicate retention,angiosperms}},
  language     = {{eng}},
  number       = {{8}},
  pages        = {{2292--2305}},
  title        = {{The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication}},
  url          = {{http://dx.doi.org/10.1093/gbe/evz156}},
  volume       = {{11}},
  year         = {{2019}},
}

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