Evidence for an ancient whole genome duplication in the cycad lineage

Danielle Roodt; Rolf Lohaus; Lieven Sterck; Riaan L Swanepoel; Yves Van de Peer; Eshchar Mizrachi

doi:10.1371/journal.pone.0184454

Evidence for an ancient whole genome duplication in the cycad lineage

PLoS One. 2017 Sep 8;12(9):e0184454. doi: 10.1371/journal.pone.0184454. eCollection 2017.

Authors

Danielle Roodt^{1

2}, Rolf Lohaus^{3

4

5}, Lieven Sterck^{3

4

5}, Riaan L Swanepoel^{1

2}, Yves Van de Peer^{2

3

4

5}, Eshchar Mizrachi^{1

2}

Affiliations

¹ Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa.
² Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa.
³ Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
⁴ VIB Center for Plant Systems Biology, Gent, Belgium.
⁵ Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.

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.

MeSH terms

Cycadopsida / classification
Cycadopsida / genetics*
Gene Duplication*
Gene Expression Profiling
Genome, Plant*
Genomics* / methods
Ginkgo biloba / genetics
Phylogeny
Transcriptome

Grants and funding

The authors acknowledge 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 for support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.