Extended Data Fig. 2: WGD in Nymphaeales.
From: The water lily genome and the early evolution of flowering plants
a, Intergenomic synteny between N. colorata (14 chromosomes), Amborella (53 longest scaffolds), and the eudicots N. nucifera (8 longest megascaffolds) and V. vinifera (19 chromosomes). Five adjacent anchor pairs were plotted as one syntenic line. Coloured lines represent one example of syntenic genes found in other species that correspond to one copy in Amborella, two in N. colorata, two in N. nucifera, and three in V. vinifera. b, KS distribution for the whole paranome of N. colorata. The light grey rectangle in the background indicates the KS boundaries used to extract duplicate pairs for absolute phylogenomic dating of the WGD event, and also highlights the range in which WGD peaks can be identified in other species of Nymphaeaceae (Supplementary Note 5.2). c, Kernel-density estimates of KS distributions for one-to-one orthologues between the outgroup species I. henryi and each of N. lutea and N. advena (red), N. colorata, N. mexicana and Nymphaea ‘Woods blue goddess’ (blue) and C. caroliniana (yellow). As each peak represents the same divergence event in the angiosperm phylogeny, the differences observed among the KS values of the peaks indicate substantial substitution rate variation among these Nymphaealean lineages (see also Fig. 2b). d, Absolute age distribution obtained from phylogenomic dating of N. colorata WGD paralogues based on orthogroups with orthologues from Amborella and G. biloba. The solid black line represents the kernel density estimate of paralogue date estimates, and the vertical dashed black line represents its peak at 107 Ma. The grey lines represent density estimates from 2,500 bootstrap replicates and the vertical black dotted lines represent the corresponding 90% confidence interval for the WGD age estimate, 117–98 Ma (see Methods). The blue histogram shows the raw distribution of divergence date estimates for paralogues.
