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Evidence for an ancient whole genome duplication in the cycad lineage

(2017) PLOS ONE. 12(9).
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.
Keywords
EXTANT GYMNOSPERMS, SEED PLANTS, MOLECULAR EVOLUTION, MAXIMUM-LIKELIHOOD, DIVERGENCE TIMES, FLOWERING PLANTS, DNA-SEQUENCES, DIVERSIFICATION, ANGIOSPERMS, ORIGIN

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Citation

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Chicago
Roodt, Danielle, Rolf Lohaus, Lieven Sterck, Riaan L Swanepoel, Yves Van de Peer, and Eshchar Mizrachi. 2017. “Evidence for an Ancient Whole Genome Duplication in the Cycad Lineage.” Plos One 12 (9).
APA
Roodt, D., Lohaus, R., Sterck, L., Swanepoel, R. L., Van de Peer, Y., & Mizrachi, E. (2017). Evidence for an ancient whole genome duplication in the cycad lineage. PLOS ONE, 12(9).
Vancouver
1.
Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. Evidence for an ancient whole genome duplication in the cycad lineage. PLOS ONE. 2017;12(9).
MLA
Roodt, Danielle, Rolf Lohaus, Lieven Sterck, et al. “Evidence for an Ancient Whole Genome Duplication in the Cycad Lineage.” PLOS ONE 12.9 (2017): n. pag. Print.
@article{8533324,
  abstract     = {Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.},
  articleno    = {e0184454},
  author       = {Roodt, Danielle and Lohaus, Rolf and Sterck, Lieven and Swanepoel, Riaan L and Van de Peer, Yves and Mizrachi, Eshchar},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {EXTANT GYMNOSPERMS,SEED PLANTS,MOLECULAR EVOLUTION,MAXIMUM-LIKELIHOOD,DIVERGENCE TIMES,FLOWERING PLANTS,DNA-SEQUENCES,DIVERSIFICATION,ANGIOSPERMS,ORIGIN},
  language     = {eng},
  number       = {9},
  pages        = {8},
  title        = {Evidence for an ancient whole genome duplication in the cycad lineage},
  url          = {http://dx.doi.org/10.1371/journal.pone.0184454},
  volume       = {12},
  year         = {2017},
}

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