Premise 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. Methods 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. Results 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. Conclusions 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.

中文翻译：

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芸苔属植物的系统发育和多个独立的全基因组复制事件

前提 全基因组重复 (WGD) 在植物的整个进化历史中普遍存在。例如，数十种 WGD 已在十字花科中进行系统发育定位，特别是在十字花科内。在十字花科的姐妹科金盏花科中也发现了 WGD 事件，但它的位置以及该目中其他科的 WGD 的位置仍不清楚。方法 生成系统转录组学数据并用于推断 74 个芸苔目分类群的核系统发育。还对其中 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十字花科主要科之间和十字花科内的关系。然后使用多种 WGD 推理方法来评估 WGD 在核系统发育中的位置。结果 提出了得到充分支持的芸苔属植物的叶绿体和核系统发育，以及金盏花科特异性 WGD 事件 Th-ɑ 的假定位置。这项工作还为先前假设的 WGD 提供了证据，包括由至少两个 Resedaceae 科成员共享的一个得到充分支持的事件，以及 Capparaceae 内的一个可能事件。结论 系统发生学和 WGD 在高度多倍体谱系中的放置仍然是一个重大挑战。这项研究通过证明采样对于 WGD 识别和系统发育位置特别重要，增加了关于 WGD 推理困难的讨论。鉴于其经济重要性和基因组资源，