Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85719, USA.
Am J Bot. 2020 Aug;107(8):1148-1164. doi: 10.1002/ajb2.1514. Epub 2020 Aug 24.
Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear.
Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny.
Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae.
Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.
全基因组复制（WGD）在植物的进化历史中普遍存在。例如，几十个 WGD 已经在 Brassicales 目内的进化枝中被系统发生定位，特别是在 Brassicaceae 科内。Cleomaceae 科也被识别出存在 WGD 事件，Cleomaceae 是 Brassicaceae 的姐妹科，但它的位置以及目内其他科的 WGD 仍然不清楚。
生成了系统发生转录组数据，并用于推断 74 个 Brassicales 分类群的核系统发育。还对其中的 66 个分类群进行了基因组调查测序，以推断叶绿体系统发育。这些系统发育用于评估和确认 Brassicales 主要科之间以及 Brassicaceae 内部的关系。然后使用多种 WGD 推断方法来评估 WGD 在核系统发育上的位置。
提出了 Brassicales 的支持良好的叶绿体和核系统发育，以及 Cleomaceae 特异的 WGD 事件 Th-ɑ 的假定位置。这项工作还为以前假设的 WGD 提供了证据，包括 Resedaceae 科中至少两个成员共享的支持良好的事件，以及 Capparaceae 科内的一个可能事件。
系统发生学和高度多倍体谱系内 WGD 的位置仍然是一个主要挑战。本研究通过证明采样对于 WGD 识别和系统发育定位特别重要，为 WGD 推断困难的讨论增添了内容。鉴于其经济重要性和基因组资源，Brassicales 仍然是评估 WGD 推断方法的理想群体。
