Evidence for an ancient whole genome duplication in the cycad lineage

RESEARCH ARTICLE Evidence for an ancient whole genome duplication in the cycad lineage Danielle Roodt1,2, Rolf Lohaus3,4,5, Lieven Sterck3,4,5, Riaan L. Swanepoel1,2, Yves Van de Peer2,3,4,5, Eshchar Mizrachi1,2* 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 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Roodt D, Lohaus R, Sterck L, Swanepoel RL, 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 Editor: Tzen-Yuh Chiang, National Cheng Kung University, TAIWAN Received: March 9, 2017 Accepted: August 24, 2017 * 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. Published: September 8, 2017 Copyright: © 2017 Roodt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Raw reads of both transcriptomes are available at the National Center for Biotechnology Information (https://www.ncbi. nlm.nih.gov/) under the submission number SUB2337915. 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 Introduction Whole genome duplications (WGDs) have been prevalent during the evolutionary history of flowering plants, and have even been linked to their origin as well as their fast rise to ecological dominance [1–3]. Furthermore, although the duplication of entire genomes is mostly regarded as an evolutionary dead-end [4–7], it has been proposed that, in times of rapid environmental change, WGDs can confer an important evolutionary advantage [8–11]. This is, for instance, suggested by the fact that many angiosperm lineages show evidence for independent WGD events around the Cretaceous-Paleogene (K-Pg) extinction ~66 million years ago (Mya) [11, 12]. Contrary to the many WGD events recorded for angiosperms, the history of the non-flowering gymnosperms paints a very different picture. Although far fewer gymnosperm species exist today compared to the angiosperms, and as such many lineages containing evidence for WGD events could have been lost, polyploidy events, ancient or more recent, in these seed PLOS ONE | https://doi.org/10.1371/journal.pone.0184454 September 8, 2017 1/8 Ancient genome duplication in the cycads 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. Competing interests: The authors have declared that no competing interests exist. plants seem rare. Thus far, Welwitschia mirabilis is the only gymnosperm showing evidence for a relatively recent WGD event [13, 14], possibly also overlapping the K-Pg boundary. In any case, this event occurred more recently than the divergence of Welwitschia from its closest relative, Gnetum (135–110 Mya) [15–17], the genome of which shows no sign of a WGD [13]. Furthermore, Ephedra, the third Gnetales genus, also lacks evidence of WGD events [13], excluding very recent duplication events that resulted in the widespread polyploidy seen in extant species of this genus [18–20]. Li et al. [13] also provided evidence for independent ancient WGDs in the conifer lineage that may have coincided with the more ancient PermianTriassic boundary, ~250 Mya. Similarly, as with the angiosperms, these conifer-specific WGDs might have contributed to the survival and success of the conifer lineage during periods of drastic environmental change [13]. The same study found evidence for an ancient WGD in the Ginkgo lineage, attributing it to the ancient WGD event proposedly shared by all seed plants [1]. Clear remnants of WGDs in cycads were not uncovered, likely due to the dearth of available public EST data [21], resulting in insufficient resolution to call an ancient WGD event in this lineage. The cycads were widespread during the Jurassic–Cretaceous, reaching their greatest diversity ~200–65 Mya [22–24]. Today, however, only a mere 348 extant species in ten genera remain [25]. The dramatic decrease in diversity was likely due to challenges such as at least three mass extinction events, as well as the arrival of, and major competition from, the angiosperms. Although the lineage itself dates back ~270 million years, most extant cycad species originated much more recently, most likely within the past 65 million years [22, 26, 27]. Therefore, the popular referral to cycads as living fossils is not entirely accurate, as the lineage itself is ancient but most species originated relatively recently. Their continued survival is somewhat paradoxical, as they have particularly slow growth and cannot compete with the fast growing, rather short-lived angiosperms. Here, we confirm that cycads have undergone an ancient WGD and show that this event was likely shared with Ginkgo biloba, preceding the divergence of these lineages. Results and discussion We sequenced transcriptome data from two tissues (see Materials and Methods) of representatives of both Encephalartos natalensis (a native cycad species from the Kwazulu-Natal province of South Africa) (...truncated)