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. 2019 Jun 6;20:458. doi: 10.1186/s12864-019-5818-7

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — 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.