A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication

Abstract

The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots.

Fig. 1

Genome structural analyses of Aquilegia and related species. a Scenario of rapid intraspecific synteny loss (diploidization) causing homoplasy of interspecific syntenies. b, c Distribution of interspecific and intraspecific syntenic blocks according to syntenic block size. d Scenario of a chromosomal fusion in the common ancestor of Aquilegia and Vitis. e Scenario of two independent chromosomal fusions in Aquilegia and Vitis, respectively. f, g Number of syntenic anchors between the orange-green fused chromosomes (Vitis chr7 and Aquilegia chr5) and their corresponding homologous regions

Fig. 2

Phylogenomic analyses of syntenic duplicates from Aquilegia. a–d Histograms and violin plots of rate-corrected Ks of gene pairs from intraspecific and interspecific synteny in Aquilegia and Nelumbo (a, b) and in Aquilegia and Vitis (c, d). Median Ks values are marked by the black line in violin plots. **p value < 0.0001. e A species tree based on a concatenated alignment of 697 strict single-copy genes. f Example gene tree supports the hypothesis of Aquilegia WGD only shared by Aquilegia and Papaver. g Example gene tree supports the hypothesis of Aquilegia WGD being Aquilegia-specific. h Example gene tree supports the hypothesis of Aquilegia WGD occurring in the ancestral eudicot. Node values: bootstraps. Branch length: the number of amino acid substitutions per site. Colored dots: WGD or triplication. Arrow: the difference in placement of the Aquilegia WGD