Whole-genome duplication (WGD) in Chinese bayberry, Myrica rubra. (a) Macrosynteny of Vitis vinifera, Myrica rubra, and Malus × domestica. Genomic alignment of V. vinifera, M. rubra, and M. × domestica shows that one ancestral region in the basal eudicot V. vinifera can be aligned to one region in M. rubra derived from the paleohexaploidization common to eudicots. One region in M. rubra can be aligned to two regions in M. × domestica, indicating that WGD recently occurred in M. × domestica. (b) Microcollinearity analysis of V. vinifera, M. rubra, and M. × domestica. These regions represent one collinear set, highlighted in orange in (a). Navy blue rectangles indicate the predicted genes in the genome. One gene in V. vinifera corresponds to one gene in M. rubra, whereas one gene in M. rubra has two homologs in M. × domestica. (c) Density distribution of fourfold synonymous third-codon transversions (4DTV) for paralogous pairs among M. rubra, M. notabilis, and V. vinifera. The single peak of the M. rubra–M. rubra paralogs indicates no recent WGD in M. rubra except for the paleohexaploidization event, which is common to eudicots.