Evidence for an ancient whole genome duplication in the cycad lineage

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dc.contributor.author Roodt, Danielle
dc.contributor.author Lohaus, Rolf
dc.contributor.author Sterck, Lieven
dc.contributor.author Swanepoel, Riaan L.
dc.contributor.author Van de Peer, Yves
dc.contributor.author Mizrachi, Eshchar
dc.date.accessioned 2017-10-30T06:26:09Z
dc.date.available 2017-10-30T06:26:09Z
dc.date.issued 2017-09-08
dc.description.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. en_ZA
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI) en_ZA
dc.description.department Genetics en_ZA
dc.description.librarian am2017 en_ZA
dc.description.sponsorship The UP Research Development Programme (RDP), the Genomics Research Institute (GRI), Multidisciplinary Research Partnership `Bioinformatics: from nucleotides to networks' Project (no. 01MR0310W) of Ghent University, and funding from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739 ± DOUBLEUP. en_ZA
dc.description.uri http://www.plosone.org en_ZA
dc.identifier.citation 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): e0184454. https://DOI. org/ 10.1371/journal.pone.0184454. en_ZA
dc.identifier.issn 1932-6203 (online)
dc.identifier.other 10.1371/journal.pone.0184454
dc.identifier.uri http://hdl.handle.net/2263/62949
dc.language.iso en en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights © 2017 Roodt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. en_ZA
dc.subject Angiosperms en_ZA
dc.subject Gymnosperms en_ZA
dc.subject Genome duplications en_ZA
dc.subject Sequenced RNA en_ZA
dc.subject Origin en_ZA
dc.subject Diversification en_ZA
dc.subject DNA sequence en_ZA
dc.subject Flowering plants en_ZA
dc.subject Divergence times en_ZA
dc.subject Maximum-likelihood en_ZA
dc.subject Molecular evolution en_ZA
dc.subject Seed plants en_ZA
dc.subject Extant gymnosperms en_ZA
dc.title Evidence for an ancient whole genome duplication in the cycad lineage en_ZA
dc.type Article en_ZA


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