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

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

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Authors

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 Dann2.Turner@uwe.ac.uk
Senior Lecturer in Molecular Biology

Matthew B. Sullivan



Abstract

© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. 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.

Journal Article Type Article
Publication Date Jun 1, 2019
Journal Nature Biotechnology
Print ISSN 1087-0156
Electronic ISSN 1546-1696
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 37
Issue 6
Pages 632-639
APA6 Citation Bin Jang, H., Bolduc, B., Zablocki, O., Kuhn, J. H., Roux, S., Adriaenssens, E. M., …Sullivan, M. B. (2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology, 37(6), 632-639. https://doi.org/10.1038/s41587-019-0100-8
DOI https://doi.org/10.1038/s41587-019-0100-8
Keywords virus classification, archaeal and bacterial virus taxonomy, scalable framework, gene-sharing networks
Publisher URL https://www.nature.com/articles/s41587-019-0100-8
Related Public URLs https://www.nature.com/articles/s41587-019-0100-8
https://u.osu.edu/viruslab/
Additional Information Additional Information : This is the author's accepted manuscript. The final published version is available here: https://www.nature.com/articles/s41587-019-0100-8

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