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Gene duplicability of core genes is highly consistent across all angiosperms

Zhen Li (UGent) , Jonas Defoort (UGent) , Setareh Tasdighian (UGent) , Steven Maere (UGent) , Yves Van de Peer (UGent) and Riet De Smet (UGent)
(2016) PLANT CELL. 28(2). p.326-344
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.
Keywords
PHYLOGENETIC ANALYSIS, FLOWERING PLANTS, PROTEIN-PROTEIN, MAXIMUM-LIKELIHOOD, DOSAGE-SENSITIVITY, ARABIDOPSIS-THALIANA, WHOLE-GENOME DUPLICATIONS, MULTIPLE SEQUENCE ALIGNMENT, NUCLEOTIDE SUBSTITUTION, EUKARYOTIC GENOMES

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Citation

Please use this url to cite or link to this publication:

Chicago
Li, Zhen, Jonas Defoort, Setareh Tasdighian, Steven Maere, Yves Van de Peer, and Riet De Smet. 2016. “Gene Duplicability of Core Genes Is Highly Consistent Across All Angiosperms.” Plant Cell 28 (2): 326–344.
APA
Li, Zhen, Defoort, J., Tasdighian, S., Maere, S., Van de Peer, Y., & De Smet, R. (2016). Gene duplicability of core genes is highly consistent across all angiosperms. PLANT CELL, 28(2), 326–344.
Vancouver
1.
Li Z, Defoort J, Tasdighian S, Maere S, Van de Peer Y, De Smet R. Gene duplicability of core genes is highly consistent across all angiosperms. PLANT CELL. 2016;28(2):326–44.
MLA
Li, Zhen, Jonas Defoort, Setareh Tasdighian, et al. “Gene Duplicability of Core Genes Is Highly Consistent Across All Angiosperms.” PLANT CELL 28.2 (2016): 326–344. Print.
@article{7244140,
  abstract     = {Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of {\textacutedbl}gene duplicability{\textacutedbl} is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.},
  author       = {Li, Zhen and Defoort, Jonas and Tasdighian, Setareh and Maere, Steven and Van de Peer, Yves and De Smet, Riet},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {PHYLOGENETIC ANALYSIS,FLOWERING PLANTS,PROTEIN-PROTEIN,MAXIMUM-LIKELIHOOD,DOSAGE-SENSITIVITY,ARABIDOPSIS-THALIANA,WHOLE-GENOME DUPLICATIONS,MULTIPLE SEQUENCE ALIGNMENT,NUCLEOTIDE SUBSTITUTION,EUKARYOTIC GENOMES},
  language     = {eng},
  number       = {2},
  pages        = {326--344},
  title        = {Gene duplicability of core genes is highly consistent across all angiosperms},
  url          = {http://dx.doi.org/10.1105/tpc.15.00877},
  volume       = {28},
  year         = {2016},
}

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