Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
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DOI：
10.1038/s41587-019-0100-8
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发表时间：
2019-06-01
影响因子：
46.9
通讯作者：
Sullivan, Matthew B.
中科院分区：
文献类型：
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作者：
Jang, Ho Bin;Bolduc, Benjamin;Sullivan, Matthew B.
来自每个环境的微生物组都包含无数未培养的古细菌和细菌病毒，但由于缺乏通用的、可扩展的分类框架，研究这些病毒受到阻碍。我们提出vConTACT v.2.0，一个基于网络的应用程序，利用全基因组基因共享配置文件的病毒分类，集成了基于距离的层次聚类和置信度得分的所有分类预测。我们报告了来自国际病毒分类学委员会国家生物技术信息中心病毒RefSeq的现有属级病毒分类分配的几乎相同（96%）的复制。将vConTACT v.2.0应用于1，364种以前未分类的病毒RefSeq作为参考基因组，为1，364种中的820种产生了自动，高置信度的属分配。我们应用vConTACT v.2.0分析了15，280个全球海洋病毒基因组片段，并能够为这些数据中的31%提供分类分配，这表明我们的算法可扩展到非常大的宏基因组数据集。我们的分类工具可以自动化并应用于任何环境中的宏基因组进行病毒分类。
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.