Supporting data for "Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions"

Polyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this paper provides expanded methodological details, results validation, and descriptions of newly released data sets that will aid researchers that wish to use the extended data generated by the 1KP project. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walkthrough examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper.

多倍体现象或全基因组复制（WGDs）在绿色植物进化过程中反复发生。为在系统基因组学框架下探究绿色植物的进化历史，1KP项目对绿色植物类群（Viridiplantae）的1000多个转录组进行了测序。1KP项目为研究全基因组复制（WGDs）在绿色植物中的分布与发生提供了独特契机。作为核心论文的补充，本文提供了扩展的方法学细节、结果验证，以及对新发布数据集的描述，这些内容将为希望使用1KP项目生成的扩展数据的研究者提供帮助。在1KP核心分析中，我们采用了总证据法（total evidence approach），结合来自同义替换率（Ks）和系统基因组学方法的全基因组复制（WGDs）推断结果，在Viridiplantae类群中鉴定并定位了244个推定的古老全基因组复制事件。本文通过详细描述方法学和示例演示，对我们的研究方法进行了扩展说明。我们还通过将全基因组复制推断结果与已发表的植物基因组组装共线性分析（syntenic analyses）证据进行比较，评估了其一致性。研究发现，我们的推断结果与全基因组共线性分析一致，且总证据法可降低整个数据集的假阳性率。鉴于这些资源对未来绿色植物基因与基因组进化的诸多分析具有重要价值，我们发布了1KP核心论文中的383,679个核基因家族系统发育树，以及2,306个附带有Ks图谱的基因年龄分布数据。