Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction
Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction
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DOI：
10.1093/sysbio/syz049
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发表时间：
2020-03-01
影响因子：
6.5
通讯作者：
Iwasaki，Wataru
中科院分区：
文献类型：
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作者：
Matsui，Motomu;Iwasaki，Wataru
蛋白质超家族包含远亲蛋白质，它们在漫长的进化历史中获得了不同的生物学功能。蛋白质超家族早期进化的系统发育分析是一个关键的挑战，因为现有的系统发育方法在蛋白质序列差异太大时表现不佳，无法构建信息丰富的多序列比对(MSA)。在这里，我们提出了图分裂(GS)方法，它使用基于图的方法快速重建蛋白质超家族规模的系统发育树。进化模拟表明，GS方法可以准确地重建系统发育树，并对系统发育估计中的主要问题具有鲁棒性，如有偏的分类单元采样、异质进化速率和当序列发生实质性差异时的长分支吸引。它应用于磷酸丙糖异构酶(TIM)桶超家族的经验数据集表明，蛋白质介导的嘧啶生物合成迅速进化，很可能发生在RNA世界之后。此外，GS方法还可以通过提供准确的指导树来显著提高广泛使用的MSA方法的性能。
A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.