Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification

Abstract

Comparative genome biology has unveiled the polyploid origin of all angiosperms and the role of recurrent polyploidization in the amplification of gene families and the structuring of genomes. Which species share certain ancient polyploidy events, and which do not, is ill defined because of the limited number of sequenced genomes and transcriptomes and their uneven phylogenetic distribution. Previously, it has been suggested that most, but probably not all, of the eudicots have shared an ancient hexaploidy event, referred to as the gamma triplication. In this study, detailed phylogenies of subfamilies of MADS-box genes suggest that the gamma triplication has occurred before the divergence of Gunnerales but after the divergence of Buxales and Trochodendrales. Large-scale phylogenetic and K(S)-based approaches on the inflorescence transcriptomes of Gunnera manicata (Gunnerales) and Pachysandra terminalis (Buxales) provide further support for this placement, enabling us to position the gamma triplication in the stem lineage of the core eudicots. This triplication likely initiated the functional diversification of key regulators of reproductive development in the core eudicots, comprising 75% of flowering plants. Although it is possible that the gamma event triggered early core eudicot diversification, our dating estimates suggest that the event occurred early in the stem lineage, well before the rapid speciation of the earliest core eudicot lineages. The evolutionary significance of this paleopolyploidy event may thus rather lie in establishing a species lineage that was resilient to extinction, but with the genomic potential for later diversification. We consider that the traits generated from this potential characterize extant core eudicots both chemically and morphologically.

Polyploidy and genome evolution in plants

“…Indeed, at some time in evolution, organisms that underwent and survived WGDs must have had an adaptive advantage. Examples of ancient WGD events that have been established on the longer term are one or two WGDs early in the evolution of seed and flowering plants (Jiao et al 2011), one WGD that is ancestral to most or all of the eudicots (Vekemans et al, 2012;Jiao et al 2012), and one or two that occurred early in the monocot lineage (Bowers et al, Paterson et al 2012). 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.…”

Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum

“…Stop criteria such as BIC (Schwarz, 1978) used in identifying the optimal number of components in the mixture are prone to overfitting (Naik et al, 2007), so that small stochastic deviations in the background SSD distribution are also often fitted (Vekemans et al, 2012). We therefore used the SiZer package (Chaudhuri and Marron, 1999) that searches for significant changes in the first derivative of a distribution in conjunction with our mixture modeling approach, as this technique allows a more robust evaluation of whether a fitted Gaussian component truly corresponds to a WGD signature .…”

Evolution of floral diversity: genomics, genes andgamma

“…Therefore, whether putative sets of gammaderived paralogues are assigned to the same orthogroup, as is necessary for phylogenomic analyses, is a matter of concern that has to be addressed post hoc. For example, only 123 of approximately 1800 gene trees analysed by Vekemans et al [83] include putative gamma-derived Vitis paralogues, and Jiao et al [44] combined orthogroups that would have otherwise kept such paralogues separate. Alternatively, in an approach that has not been attempted to date, the syntenybased orthogroups circumscribed for Vitis [43] may be used as a reference to which genes from other species can be assigned, facilitating phylogenomics within the prescribed context of putative gamma-derived paralogues.…”