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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Riet De Smet (UGent) , Keith L Adams, Klaas Vandepoele (UGent) , Marc Van Montagu (UGent) , Steven Maere (UGent) and Yves Van de Peer (UGent)
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.
Keywords
AGE DISTRIBUTIONS, ARABIDOPSIS, NUCLEAR GENES, EVOLUTION, BALANCE HYPOTHESIS, WHOLE-GENOME, DOSAGE-SENSITIVITY, EUKARYOTIC GENOMES, SYNONYMOUS CODON USAGE, DOMINANT-NEGATIVE MUTATIONS

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Chicago
De Smet, Riet, Keith L Adams, Klaas Vandepoele, Marc Van Montagu, Steven Maere, and Yves Van de Peer. 2013. “Convergent Gene Loss Following Gene and Genome Duplications Creates Single-copy Families in Flowering Plants.” Proceedings of the National Academy of Sciences of the United States of America 110 (8): 2898–2903.
APA
De Smet, Riet, Adams, K. L., Vandepoele, K., Van Montagu, M., Maere, S., & Van de Peer, Y. (2013). Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(8), 2898–2903.
Vancouver
1.
De Smet R, Adams KL, Vandepoele K, Van Montagu M, Maere S, Van de Peer Y. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013;110(8):2898–903.
MLA
De Smet, Riet, Keith L Adams, Klaas Vandepoele, et al. “Convergent Gene Loss Following Gene and Genome Duplications Creates Single-copy Families in Flowering Plants.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110.8 (2013): 2898–2903. Print.
@article{3194024,
  abstract     = {The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.},
  author       = {De Smet, Riet and Adams, Keith L and Vandepoele, Klaas and Van Montagu, Marc and Maere, Steven and Van de Peer, Yves},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  language     = {eng},
  number       = {8},
  pages        = {2898--2903},
  title        = {Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants},
  url          = {http://dx.doi.org/10.1073/pnas.1300127110},
  volume       = {110},
  year         = {2013},
}

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