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The hidden duplication past of Arabidopsis thaliana

Cedric Simillion (UGent) , Klaas Vandepoele (UGent) , Marc Van Montagu (UGent) , Marc Zabeau (UGent) and Yves Van de Peer (UGent)
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Abstract
Analysis of the genome sequence of Arabidopsis thaliana shows that this genome, like that of many other eukaryotic organisms, has undergone large-scale gene duplications or even duplications of the entire genome. However, the high frequency of gene loss after duplication events reduces colinearity and therefore the chance of finding duplicated regions that, at the extreme, no longer share homologous genes. In this study we show that heavily degenerated block duplications that can no longer be recognized by directly comparing two segments because of differential gene loss, can still be detected through indirect comparison with other segments. When these so-called hidden duplications in Arabidopsis are taken into account, many homologous genomic regions can be found in five to eight copies. This finding strongly implies that Arabidopsis has undergone three, but probably no more, rounds of genome duplications. Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past.
Keywords
SYNTENY, RATES, SEQUENCE, POLYPLOIDY, GENES, EVOLUTION, GENOME, CHROMOSOMAL DUPLICATION, NONSYNONYMOUS SUBSTITUTION

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Chicago
Simillion, Cedric, Klaas Vandepoele, Marc Van Montagu, Marc Zabeau, and Yves Van de Peer. 2002. “The Hidden Duplication Past of Arabidopsis Thaliana.” Proceedings of the National Academy of Sciences of the United States of America 99 (21): 13627–13632.
APA
Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M., & Van de Peer, Y. (2002). The hidden duplication past of Arabidopsis thaliana. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99(21), 13627–13632.
Vancouver
1.
Simillion C, Vandepoele K, Van Montagu M, Zabeau M, Van de Peer Y. The hidden duplication past of Arabidopsis thaliana. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002;99(21):13627–32.
MLA
Simillion, Cedric, Klaas Vandepoele, Marc Van Montagu, et al. “The Hidden Duplication Past of Arabidopsis Thaliana.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 99.21 (2002): 13627–13632. Print.
@article{154053,
  abstract     = {Analysis of the genome sequence of Arabidopsis thaliana shows that this genome, like that of many other eukaryotic organisms, has undergone large-scale gene duplications or even duplications of the entire genome. However, the high frequency of gene loss after duplication events reduces colinearity and therefore the chance of finding duplicated regions that, at the extreme, no longer share homologous genes. In this study we show that heavily degenerated block duplications that can no longer be recognized by directly comparing two segments because of differential gene loss, can still be detected through indirect comparison with other segments. When these so-called hidden duplications in Arabidopsis are taken into account, many homologous genomic regions can be found in five to eight copies. This finding strongly implies that Arabidopsis has undergone three, but probably no more, rounds of genome duplications. Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past.},
  author       = {Simillion, Cedric and Vandepoele, Klaas and Van Montagu, Marc and Zabeau, Marc and Van de Peer, Yves},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keyword      = {SYNTENY,RATES,SEQUENCE,POLYPLOIDY,GENES,EVOLUTION,GENOME,CHROMOSOMAL DUPLICATION,NONSYNONYMOUS SUBSTITUTION},
  language     = {eng},
  number       = {21},
  pages        = {13627--13632},
  title        = {The hidden duplication past of Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1073/pnas.212522399},
  volume       = {99},
  year         = {2002},
}

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