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Modeling gene and genome duplications in eukaryotes

Steven Maere UGent, Stefanie De Bodt UGent, Jeroen Raes, Tineke Casneuf, Marc Van Montagu UGent, Martin Kuiper and Yves Van de Peer UGent (2005) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 102(15). p.5454-5459
abstract
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
functional categories, Arabidopsis, gene retention, PHYLOGENETIC ANALYSIS, ARABIDOPSIS-THALIANA, EVOLUTION, SENSITIVITY, DIVERGENCE, POLYPLOIDY
journal title
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Proc. Natl. Acad. Sci. USA
volume
102
issue
15
pages
5454 - 5459
Web of Science type
Article
Web of Science id
000228376600031
JCR category
MULTIDISCIPLINARY SCIENCES
JCR impact factor
10.231 (2005)
JCR rank
3/47 (2005)
JCR quartile
1 (2005)
ISSN
0027-8424
DOI
10.1073/pnas.0501102102
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
336524
handle
http://hdl.handle.net/1854/LU-336524
date created
2006-05-31 17:24:00
date last changed
2012-12-19 16:08:33
@article{336524,
  abstract     = {Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for {\textrangle}90\% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.},
  author       = {Maere, Steven and De Bodt, Stefanie and Raes, Jeroen and Casneuf, Tineke and Van Montagu, Marc and Kuiper, Martin and Van de Peer, Yves},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keyword      = {functional categories,Arabidopsis,gene retention,PHYLOGENETIC ANALYSIS,ARABIDOPSIS-THALIANA,EVOLUTION,SENSITIVITY,DIVERGENCE,POLYPLOIDY},
  language     = {eng},
  number       = {15},
  pages        = {5454--5459},
  title        = {Modeling gene and genome duplications in eukaryotes},
  url          = {http://dx.doi.org/10.1073/pnas.0501102102},
  volume       = {102},
  year         = {2005},
}

Chicago
Maere, Steven, Stefanie De Bodt, Jeroen Raes, Tineke Casneuf, Marc Van Montagu, Martin Kuiper, and Yves Van de Peer. 2005. “Modeling Gene and Genome Duplications in Eukaryotes.” Proceedings of the National Academy of Sciences of the United States of America 102 (15): 5454–5459.
APA
Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., & Van de Peer, Y. (2005). Modeling gene and genome duplications in eukaryotes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(15), 5454–5459.
Vancouver
1.
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, et al. Modeling gene and genome duplications in eukaryotes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2005;102(15):5454–9.
MLA
Maere, Steven, Stefanie De Bodt, Jeroen Raes, et al. “Modeling Gene and Genome Duplications in Eukaryotes.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102.15 (2005): 5454–5459. Print.