Microbiology and Infectious Disease

Research: A comprehensive and quantitative exploration of thousands of viral genomes

California Institute of Technology, United States

Apr 6, 2018

https://doi.org/10.7554/eLife.31955

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Abstract

The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there still remain significant blind spots in our view of viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.

Data availability

All source data, scripts and output data used to create this manuscript is deposited in our manuscript, its supporting files and our GitHub repository : https://github.com/gitamahm/VirologyByTheNumbers

The following previously published data sets were used

(2015) NCBI viral genomes resource
Publicly available at the NCBI viral resource page (https://www.ncbi.nlm.nih.gov/genome/viruses/).

ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

Article and author information

Author details

Gita Mahmoudabadi

Department of Bioengineering, California Institute of Technology, Pasadena, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8812-7246
Rob Phillips

Department of Bioengineering, California Institute of Technology, Pasadena, United States

For correspondence
phillips@pboc.caltech.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3082-2809

Funding

John Templeton Foundation (51250)

Rob Phillips

National Institutes of Health (RFA-GM-17-002)

Rob Phillips

National Science Foundation (DGE‐1144469)

Gita Mahmoudabadi

National Institutes of Health (R01- GM098465)

Rob Phillips

National Science Foundation (NSF PHY11-25915)

Rob Phillips

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.