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Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana

Riet De Smet (UGent) , Ehsan Sabaghian (UGent) , Zhen Li (UGent) , Yvan Saeys (UGent) and Yves Van de Peer (UGent)
(2017) PLANT CELL. 29(11). p.2786-2800
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub-or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress.
Keywords
YEAST TRANSCRIPTIONAL NETWORK, MULTIPLE SEQUENCE ALIGNMENT, PLANT-CELL, WALL, EVOLUTIONARY NOVELTY, WHOLE-GENOME, POLLEN TUBES, PHYLOGENETIC, ANALYSIS, REGULATORY EVOLUTION, ACTIN ORGANIZATION, PHOSPHATIDIC-ACID

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Citation

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Chicago
De Smet, Riet, Ehsan Sabaghian, Zhen Li, Yvan Saeys, and Yves Van de Peer. 2017. “Coordinated Functional Divergence of Genes After Genome Duplication in Arabidopsis Thaliana.” Plant Cell 29 (11): 2786–2800.
APA
De Smet, Riet, Sabaghian, E., Li, Z., Saeys, Y., & Van de Peer, Y. (2017). Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana. PLANT CELL, 29(11), 2786–2800.
Vancouver
1.
De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y. Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana. PLANT CELL. 2017;29(11):2786–800.
MLA
De Smet, Riet, Ehsan Sabaghian, Zhen Li, et al. “Coordinated Functional Divergence of Genes After Genome Duplication in Arabidopsis Thaliana.” PLANT CELL 29.11 (2017): 2786–2800. Print.
@article{8543588,
  abstract     = {Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub-or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress.},
  author       = {De Smet, Riet and Sabaghian, Ehsan and Li, Zhen and Saeys, Yvan and Van de Peer, Yves},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {YEAST TRANSCRIPTIONAL NETWORK,MULTIPLE SEQUENCE ALIGNMENT,PLANT-CELL,WALL,EVOLUTIONARY NOVELTY,WHOLE-GENOME,POLLEN TUBES,PHYLOGENETIC,ANALYSIS,REGULATORY EVOLUTION,ACTIN ORGANIZATION,PHOSPHATIDIC-ACID},
  language     = {eng},
  number       = {11},
  pages        = {2786--2800},
  title        = {Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1105/tpc.17.00531},
  volume       = {29},
  year         = {2017},
}

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