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Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions.
GigaScience ( IF 11.8 ) Pub Date : 2020-02-01 , DOI: 10.1093/gigascience/giaa004
Zheng Li 1 , Michael S Barker 1
Affiliation  

BACKGROUND 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 >1,000 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 article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. RESULTS 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 walk-through 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 dataset. CONCLUSIONS We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

中文翻译:


推断 1000 种植物 (1KP) 计划中假定的古代全基因组重复:获取基因家族系统发育和年龄分布。



背景技术多倍体或全基因组重复(WGD)在绿色植物进化过程中反复发生。为了在系统基因组框架中研究绿色植物的进化历史,1KP 项目对 Viridiplantae 的超过 1,000 个转录组进行了测序。 1KP 项目提供了一个独特的机会来研究 WGD 在绿色植物中的分布和发生。作为顶点出版物的补充,本文提供了扩展的方法细节、结果验证和新发布的数据集的描述,这将帮助希望使用 1KP 项目生成的扩展数据的研究人员。结果在 1KP 顶点分析中,我们使用了一种总证据方法,该方法结合了 Ks 的 WGD 推论和系统发育学方法,以推断并放置了 Viridiplantae 中的 244 个假定的古代 WGD。在这里,我们通过描述我们的方法和演练示例来对我们的方法进行扩展解释。我们还通过将 WGD 推论与已发表的植物基因组组装同线性分析的证据进行比较来评估其一致性。我们发现我们的推论与全基因组同线性分析一致,并且我们的总证据方法可以最大限度地减少整个数据集中的假阳性率。结论 我们发布了 383,679 个核基因家族系统发育和 2,306 个基因年龄分布以及 1KP 顶点论文中的 Ks 图。这些资源将有助于未来对绿色植物基因和基因组进化的许多分析。
更新日期:2020-02-11
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