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Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

Tineke Casneuf, Stefanie De Bodt UGent, Jeroen Raes, Steven Maere UGent and Yves Van de Peer UGent (2006) GENOME BIOLOGY. 7(2).
abstract
Background: Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. Results: Duplicates that have been created by large- scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. Conclusion: By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PHYLOGENETIC ANALYSIS, FUNCTIONAL DIVERGENCE, EVOLUTIONARY FATE, MICROARRAY DATA, PROBE LEVEL, POLYPLOIDY, DOMAINS, RATES, SUBFUNCTIONALIZATION, NORMALIZATION
journal title
GENOME BIOLOGY
Genome Biol.
volume
7
issue
2
article_number
R13
pages
11 pages
Web of Science type
Article
Web of Science id
000237298500010
ISSN
1474-7596
DOI
10.1186/gb-2006-7-2-r13
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
371616
handle
http://hdl.handle.net/1854/LU-371616
date created
2007-07-03 17:29:00
date last changed
2012-12-11 16:28:02
@article{371616,
  abstract     = {Background: Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. 
Results: Duplicates that have been created by large- scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. 
Conclusion: By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.},
  articleno    = {R13},
  author       = {Casneuf, Tineke and De Bodt, Stefanie and Raes, Jeroen and Maere, Steven and Van de Peer, Yves},
  issn         = {1474-7596},
  journal      = {GENOME BIOLOGY},
  keyword      = {PHYLOGENETIC ANALYSIS,FUNCTIONAL DIVERGENCE,EVOLUTIONARY FATE,MICROARRAY DATA,PROBE LEVEL,POLYPLOIDY,DOMAINS,RATES,SUBFUNCTIONALIZATION,NORMALIZATION},
  language     = {eng},
  number       = {2},
  pages        = {11},
  title        = {Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1186/gb-2006-7-2-r13},
  volume       = {7},
  year         = {2006},
}

Chicago
Casneuf, Tineke, Stefanie De Bodt, Jeroen Raes, Steven Maere, and Yves Van de Peer. 2006. “Nonrandom Divergence of Gene Expression Following Gene and Genome Duplications in the Flowering Plant Arabidopsis Thaliana.” Genome Biology 7 (2).
APA
Casneuf, T., De Bodt, S., Raes, J., Maere, S., & Van de Peer, Y. (2006). Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. GENOME BIOLOGY, 7(2).
Vancouver
1.
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. GENOME BIOLOGY. 2006;7(2).
MLA
Casneuf, Tineke, Stefanie De Bodt, Jeroen Raes, et al. “Nonrandom Divergence of Gene Expression Following Gene and Genome Duplications in the Flowering Plant Arabidopsis Thaliana.” GENOME BIOLOGY 7.2 (2006): n. pag. Print.