Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales

Abstract

Background and aims: To assess the number and phylogenetic distribution of large-scale genome duplications in the ancestry of Actinidia, publicly available expressed sequenced tags (ESTs) for members of the Actinidiaceae and related Ericales, including tea (Camellia sinensis), were analysed.

Methods: Synonymous divergences (K(s)) were calculated for all duplications within gene families and examined for evidence of large-scale duplication events. Phylogenetic comparisons for a selection of orthologues among several related species in Ericales and two outgroups permitted placement of duplication events in relation to lineage divergences. Gene ontology (GO) categories were analysed for each whole-genome duplication (WGD) and the whole transcriptome.

Key results: Evidence for three ancient WGDs in Actinidia was found. Analyses of paleologue GO categories indicated a different pattern of retained genes for each genome duplication, but a pattern consistent with the dosage-balance hypothesis among all retained paleologues.

Conclusions: This study provides evidence for one independent WGD in the ancestry of Actinidia (Ad-alpha), a WGD shared by Actinidia and Camellia (Ad-beta), and the well-established At-gamma WGD that occurred prior to the divergence of all taxa examined. More ESTs in other taxa are needed to elucidate which groups in Ericales share the Ad-beta or Ad-alpha duplications and their impact on diversification.

Fig. 1.

Histograms of the age distribution of gene duplications from (A) Actinidia chinensis, (B) Actinidia deliciosa, (C) Actinidia eriantha, (D) Camellia sinensis and (E) Diospyros kaki. Shaded distributions represent mixture model fits of inferred whole genome duplications: red = Ad-α, blue = Ad-β, green = putative At-γ, and grey = possible duplication.

Fig. 2.

Phylogeny of Ericales taxa and related Rosid outgroups displaying inferred paleopolyploidizations. Branch lengths are mean K_s values from 37 nuclear orthologues (see Table S2, available online). Coloured dots indicate inferred paleopolyploidizations placed in relation to lineage divergence base on the rate corrections. The ‘?’ represents an ambiguous paleopolyploidization inferred from Diospyros ESTs.

Fig. 3.

GO annotations of Actinidia non-paleologues and paleologues. The colour enrichment represents the normalized unigene number of each GO slim category in the pooled Actinidia non-paleologues and paleologues. The GO slim category patterns among non-paleologues and paleologues were revealed by complete linkage hierarchical clustering. Boxes reflect relative level of GO category representation from low (green) to high (red).