Evidence for an ancient whole genome duplication in the cycad lineage

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.

A genome for gnetophytes and early evolution of seed plants

“…In addition, a WGD event has been proposed at the base of all seed plants approximately 341 Ma (zeta WGD 27 ), although the underlying evidence for these two ancient WGD events has been recently questioned 28 . In gymnosperms, WGDs have been reported for conifers, G. biloba and cycads (a likely shared WGD) 14,29,30 . Although recent polyploidy seems common in extant Ephedra 31 , evidence for ancient WGDs in gnetophytes is missing (Supplementary Information and Supplementary Fig.…”

RADseq as a valuable tool for plants with large genomes—A case study in cycads

“…Plant genome sizes are highly plastid (Pellicer, Hidalgo, Dodsworth, & Leitch, ), ranging from 13.2 Megabase pairs (Mbp) in the genome of Ostreococcus lucimarinus to over 149 Gigabase pairs (Gbp) in the octoploid Paris japonica (Pellicer, Fay, & Leitch, ). As a result of whole genome duplication, gymnosperm genomes are generally larger than those found in many angiosperms, ranging from ~8 Gbp in Microstrobus to ~72 Gbp in Pinus and Ceratozamia (Roodt et al, ; Scott, Stenz, Ingvarsson, & Baum, ; Zonneveld, , ; Zonneveld & Lindstrom, ). Typically, as a result of polyploidy, the on‐average large genome size is caused by an inefficiency of gymnosperms at eliminating repeat amplifications in the genome (Pellicer et al, ).…”

“…In order to test the effectiveness of RADseq for taxa with large genomes, we used a RADseq technique across a cohort of samples representing ten known cycad genera (Cycadales). We chose cycads because they have particularly large genomes, ranging from ~25 to 30 Gbp in Cycas L. to ~72 Gbp in Ceratozamia (Zonneveld, ), which appears to be the result of many tandem repeats, pseudogenes, paralogs and possibly whole genome duplication (Roodt et al, ). In addition to having on‐average larger genomes, we also chose cycads because there is need for better methods to find more data‐rich sequences for the purposes of systematic and population genomic studies.…”

“…in Microstrobus to ~72 Gbp in Pinus and Ceratozamia (Roodt et al, 2017;Scott, Stenz, Ingvarsson, & Baum, 2016;Zonneveld, 2012aZonneveld, , 2012bZonneveld & Lindstrom, 2016). Typically, as a result of polyploidy, the on-average large genome size is caused by an inefficiency of gymnosperms at eliminating repeat amplifications in the genome (Pellicer et al, 2018).…”

“…Gbp in Cycas L. to ~72 Gbp in Ceratozamia (Zonneveld, 2012a), which appears to be the result of many tandem repeats, pseudogenes, paralogs and possibly whole genome duplication (Roodt et al, 2017).…”