Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes
Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes
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DOI：
10.1093/gbe/evaa198
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发表时间：
2020-12-01
影响因子：
3.3
通讯作者：
Katz, Laura A.
中科院分区：
文献类型：
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作者：
Weiner, Agnes K. M.;Ceron-Romero, Mario A.;Katz, Laura A.
真核生物中的表观遗传过程通过调控基因表达、染色质结构和基因组重排发挥重要作用。染色质修饰的作用（例如，DNA甲基化和组蛋白修饰）和非蛋白质编码的RNA已经在动物和植物中得到了很好的研究。除了少数模式生物（例如，酵母菌和疟原虫），对真核生物生命树其余部分的表观遗传工具包知之甚少。即使数据有限，以前的工作表明在最后一个真核生物共同祖先中存在一个古老的表观遗传工具包。我们使用PhyloToL，我们的分类丰富的基因组管道，检测表观遗传基因的同源物，并评估它们在真核生物中的宏观进化模式。除了来自基因库的数据之外，我们还通过添加来自纤毛虫、有孔虫和有壳变形虫的新单细胞转录组，增加了对SAR（Stramenopila、Alveolata和Rhizaria）和阿米巴原虫等未充分研究的分支的分类单元采样。我们专注于118个基因家族，其中94个参与染色质修饰，24个参与非蛋白质编码RNA过程。我们的研究结果表明：1）在最后一个真核生物共同祖先中存在大量的表观遗传基因家族; 2）主要真核生物分支之间的差异保守性，在Excavata中的基因显着缺乏; 3）表观遗传基因家族在物种之间的点状分布与快速进化一致，导致基因丢失。总之，这些数据证明了分类单元丰富的表观基因组研究在> 10亿年进化尺度上阐明进化模式的力量，并表明宏观进化现象，如基因组冲突，塑造了真核表观遗传工具包的进化。
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of > 1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.