近日，美国俄亥俄州立大学的Matthew B. Sullivan研究组开发了一个基因共享网络用于未知原核病毒基因组的分类。这一研究成果于2019年6月发表在国际知名学术期刊《Nature Biotechnology》上。

研究人员开发了一个名为vConTACT v.2.0的工具，这是一种基于网络的应用程序通过使用全基因组基因共享信息对病毒分类。这个工具整合了基于距离的层次聚类并对所有分类预测置信度进行评分。通过对NCBI已收录的病毒种属分类进行测试，研究人员得到了与数据库近乎一致的结果（96%）。利用该软件对1364种已收录但未分类的病毒进行测试，研究人员得到了其中820种病毒的自动、可信的种属分类结果。此外，研究人员利用该软件分析了15280个全球海洋病毒组的基因组片段，并为其中31%的数据提供了分类结果。由此表明，这一算法可扩展至非常巨大的元基因组数据分析。总之，这个工具能够为来自任何环境的病毒元基因组进行自动分类。

据介绍，来自各种环境的微生物群体包含了大量未知古菌和细菌的病毒，但对这些病毒的研究却受限于缺乏一种通用的、可扩展的分类框架。

Title: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author: Ho Bin Jang, Benjamin Bolduc, Olivier Zablocki, Jens H. Kuhn, Simon Roux, Evelien M. Adriaenssens, J. Rodney Brister, Andrew M Kropinski, Mart Krupovic, Rob Lavigne, Dann Turner, Matthew B. Sullivan

Issue&Volume: Volume 37 Issue 6, June 2019

Abstract: 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.

DOI: 10.1038/s41587-019-0100-8

Source:https://www.nature.com/articles/s41587-019-0100-8