A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication
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A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication Tao Shi1,2*
and Jinming Chen1,2*
This comment refers to the article available at https://doi.org/10.1186/ s13059-020-02211-z. * Correspondence: shitao323@ wbgcas.cn; [email protected] Please see the related Aköz and Nordborg article: www.dx.doi.org/1 0.1186/s13059-019-1888-8. 1 Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China Full list of author information is available at the end of the article
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.
Whole-genome duplications (WGDs) are frequent and common in plants, contributing to the evolutionary novelty and adaptation to extreme environments [1, 2]. Aköz and Nordborg reported a common WGD in the ancestral eudicot: while this ancestral tetraploid is preserved in Aquilegia (a basal eudicot), the hexaploid in the ancestral core eudicot was formed by hybridization of this tetraploid and another diploid with a subsequent WGD [3]. Nevertheless, this is contradictory to the studies of Nelumbo nucifera [4, 5]. Nelumbo, another basal eudicot, having a much closer relationship with core eudicots [6], shows a slower synteny loss and substitution rate than Aquilegia and core eudicots when aligned to outgroup species including Nymphaea colorata [7], rice, and Brachypodium distachyon (Figs. 1b and 2e) [4], and thus, Nelumbo should preserve more of its traces. However, the Ks peak corresponding to the “shared WGD” is absent in Nelumbo, and only a lineage-specific WGD after the Nelumbo-Macadamia split was found [4] (Fig. 2a), which raises doubt about their hypothesis of the common tetraploid origin. The authors’ assertion that the Aquilegia WGD is shared by all eudicots is mainly based on clustering by gene order similarity or structural similarity within species genome and between species, which depends on synteny evolutionary rate. When the trait evolves with rate heterogeneity, the simple clustering by similarity can hardly reflect the true phylogeny. Therefore, the more rapid loss of intraspecific synteny in Aquilegia might cause homoplasy such that higher similarity in gene order of Aquilegia-Vitis than Aquilegia-Aquilegia can be observed (Fig. 1a). Indeed, Aquilegia-Aquilegia shows the most rapid decay of synteny with the smallest size and the fewest number of syntenic blocks, which is even smaller and fewer than older divergent pairs (Aquilegia-Ceratophyllum and © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to
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