Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
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DOI：
10.1093/sysbio/syz036
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发表时间：
2020-01-01
影响因子：
6.5
通讯作者：
Adriaenssens, Evelien M.
中科院分区：
文献类型：
--
作者：
Barylski, Jakub;Enault, Francois;Adriaenssens, Evelien M.
拖尾噬菌体是世界上最丰富和最多样化的病毒，基因组大小从10kbp到超过500kbp不等。然而，由于历史原因，所有这些多样性仅限于一个单一的病毒目-尾状病毒科，仅由四个科组成：肌病毒科、剑鱼科、斑点病毒科和新创建的阿克曼病毒科。近年来，这种基于形态的分类方案已经开始在源源不断的噬菌体序列的洪流下崩溃，揭示出尾巴噬菌体的基因多样性甚至比人们曾经认为的更加多样化。这促使我们，即国际病毒分类委员会(ICTV)的细菌和古细菌病毒小组委员会，考虑对噬菌体分类进行全面重组。在这项研究中，我们使用了广泛的互补方法-包括比较基因组学、核心基因组分析和标记基因系统发育学-表明与芽孢杆菌噬菌体SPO1相关的病毒群以前被归入Spounavirinae亚家族，明显有别于Myoviridae家族的其他成员，其多样性值得被列为自治家族。因此，我们将这一组从Myoviridae家族中移除，并创建了Herelleviridae家族--一个相同等级的新分类单元。在分类群评估的过程中，我们探索了不同划分标准的可行性，并对我们的噬菌体分类方法的有效性进行了批判性评估。结果的收敛，绘制了一个新的科和相关的亚科的一致和全面的图景，无论采用什么方法，表明这里应用的工具在噬菌体分类中特别有用。我们相信，这个新的家族的创建是一个重要的里程碑，朝着尾孢子目中亟需的重新分类迈进。
Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.