PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes
PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes
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DOI：
10.1093/molbev/msz103
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发表时间：
2019-08-01
影响因子：
10.7
通讯作者：
Katz, L. A.
中科院分区：
文献类型：
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作者：
Ceron-Romero, Mario A.;Maurer-Alcala, Xyrus X.;Katz, L. A.
多序列比对(MSA)的估计和系统发育的推断是比较生物学的重要方面。然而，许多用于这类分析的生物信息学工具都集中在特定的分支上，最关注的是植物、动物和真菌。来自不同谱系的高通量测序(HTS)数据的快速增长现在为估计真核生物生命树上的进化关系和基因家族进化提供了机会。同时，众所周知，这些类型的数据容易出错(例如，替换、污染)。为了应对这些机遇和挑战，我们改进了一条系统基因组学管道，现在命名为PhyloToL，以便轻松整合HTS研究的数据，实现MSA和基因树的自动化生产，并识别和去除污染物。PhyloToL是为生命之树上不同血统的系统学分析而设计的(即，在>；100 My的尺度上)。我们通过评估纤毛纲停止密码子的使用，在分类群和基因丰富的数据库中识别污染，以及探索动质寄生虫布鲁氏锥虫的染色体进化史，展示了PhyloToL的力量。布氏锥虫是非洲昏睡病的病原体。将PhyloToL的同源性评估与OrthoMCL的同源性评估和一篇关于细菌和真核细胞器外膜孔形成蛋白超家族的论文进行了比较，证明了我们的方法在确定基因家族成员和推断基因树方面的强大功能。PhyloToL高度灵活，允许用户轻松探索HTS数据，测试有关系统发育和基因家族进化的假设，并将输出与第三方工具(如PhyloChromoMap、IGTP)相结合。
Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential formany aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation of data from HTS studies, to automate production of both MSAs and gene trees, and to identify and remove contaminants. PhyloToL is designed for phylogenomic analyses of diverse lineages across the tree of life (i.e., at scales of >100 My). We demonstrate the power of PhyloToL by assessing stop codon usage in Ciliophora, identifying contamination in a taxon- and gene-rich database and exploring the evolutionary history of chromosomes in the kinetoplastid parasite Trypanosoma brucei, the causative agent of African sleeping sickness. Benchmarking PhyloToL's homology assessment against that of OrthoMCL and a published paper on superfamilies of bacterial and eukaryotic organellar outer membrane pore-forming proteins demonstrates the power of our approach for determining gene family membership and inferring gene trees. PhyloToL is highly flexible and allows users to easily explore HTS data, test hypotheses about phylogeny and gene family evolution and combine outputs with third-party tools (e.g., PhyloChromoMap, iGTP).