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Evidence for an ancient whole genome duplication in the cycad lineage

Danielle Roodt, Rolf Lohaus UGent, Lieven Sterck UGent, Riaan L Swanepoel, Yves Van de Peer UGent and Eshchar Mizrachi (2017) PLOS ONE. 12(9).
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
EXTANT GYMNOSPERMS, SEED PLANTS, MOLECULAR EVOLUTION, MAXIMUM-LIKELIHOOD, DIVERGENCE TIMES, FLOWERING PLANTS, DNA-SEQUENCES, DIVERSIFICATION, ANGIOSPERMS, ORIGIN
journal title
PLOS ONE
PLoS One
volume
12
issue
9
article number
e0184454
pages
8 pages
Web of Science type
Article
Web of Science id
000410001100124
ISSN
1932-6203
DOI
10.1371/journal.pone.0184454
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8533324
handle
http://hdl.handle.net/1854/LU-8533324
date created
2017-10-05 13:48:14
date last changed
2018-03-22 12:47:02
@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},
}

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.