Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum

Abstract

Horsetails represent an enigmatic clade within the land plants. Despite consisting only of one genus (Equisetum) that contains 15 species, they are thought to represent the oldest extant genus within the vascular plants dating back possibly as far as the Triassic. Horsetails have retained several ancient features and are also characterized by a particularly high chromosome count (n = 108). Whole-genome duplications (WGDs) have been uncovered in many angiosperm clades and have been associated with the success of angiosperms, both in terms of species richness and biomass dominance, but remain understudied in nonangiosperm clades. Here, we report unambiguous evidence of an ancient WGD in the fern linage, based on sequencing and de novo assembly of an expressed gene catalog (transcriptome) from the giant horsetail (Equisetum giganteum). We demonstrate that horsetails underwent an independent paleopolyploidy during the Late Cretaceous prior to the diversification of the genus but did not experience any recent polyploidizations that could account for their high chromosome number. We also discuss the specific retention of genes following the WGD and how this may be linked to their long-term survival.

Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny

“…These results are consistent with the evidence for a WGD in the common ancestor of the extant horsetails detected in transcriptome data (Vanneste et al, 2015).…”

“…Nevertheless, recent transcriptome data for the horsetail Equisetum giganteum is not inconsistent with multiple WGD events contributing to the high chromosome numbers in this species (2n = 216; Vanneste et al, 2015).…”

Field Guide to Plant Model Systems

“…Ferns evolved leaves independently of seed plants, and whether the molecular mechanisms are similar is actively being investigated (Plackett et al, 2015). Ferns are often polyploids with large genomes, and while no draft fern genome sequences are currently available (Wolf et al, 2015), transcriptome assemblies of Azolla filiculoides (an aquatic fern; genome of 740 Mb) and Equisetum giganteum (horsetail) have provided some insight into gene content (Vanneste et al, 2015; Brouwer et al, 2014). A derived fern, Ceratopteris richardii (11.26 Gb) has been developed to some extent as a model system with genetic approaches; e.g., investigations of sex determination mechanisms (Strain et al, 2001; Atallah and Banks, 2015) and transformation protocols have been established (Muthukumar et al, 2013; Plackett et al, 2014).…”

Polyploidy and genome evolution in plants

“…Therefore, a question that has received much attention of late is whether these key ancient WGDs, which in many cases characterize major lineages of flowering plants, have survived by coincidence, or whether they may have originated in concert, at very specific geological times, for instance during times of major ecological or environmental upheaval, and/or periods of extinction. In this respect, one of the most striking cases is a wave of WGDs in different flowering plant lineages that seem to coincide with the Cretaceous/Paleogene (K/Pg) boundary (Fawcett et al, 2009;Vanneste et al, 2014a, b;Vanneste et al, 2015;Ciao et al, 2015;Olsen et al, 2015). Furthermore, many of the WGDs clustered around the K/Pg extinction event are at the base of some of the largest and most successful extant plant families.…”