Evidence for an ancient whole genome duplication in the cycad lineage

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

Evidence for an ancient whole genome duplication in the cycad lineage

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.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.http://www.plosone.orgam2017Forestry and Agricultural Biotechnology Institute (FABI)Genetic

<i>K</i>_S age distributions for <i>Ginkgo biloba</i> and <i>Encephalartos natalensis</i> transcriptomes.

<p>The red graph represents the age distribution of duplicates (in the transcriptome) of <i>G</i>. <i>biloba</i>, while the blue graph represents the age distribution of duplicates of <i>E</i>. <i>natalensis</i>. The graph in grey denotes the <i>K</i>_S distribution for one-to-one orthologs of <i>G</i>. <i>biloba</i> and <i>E</i>. <i>natalensis</i>.</p

Possible locations for the whole genome duplication uncovered for <i>Encephalartos natalensis</i> and <i>Ginkgo biloba</i>.

<p>Cycad and ginkgo share a common ancestor and are sister to the ancestor of Gnetales and conifers [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref017" target="_blank">17</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref030" target="_blank">30</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref034" target="_blank">34</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref035" target="_blank">35</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref037" target="_blank">37</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184454#pone.0184454.ref039" target="_blank">39</a>]: the inferred polyploidy event could have occurred in the common ancestor of the cycad and gingko lineages (red square), the gymnosperm ancestor (green square), or in the seed plant ancestor (blue square). Note that the position of Gnetales remains uncertain (see text for details).</p