1. Microbiology and Infectious Disease
Download icon

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

  1. Gita Mahmoudabadi
  2. Rob Phillips  Is a corresponding author
  1. California Institute of Technology, United States
Feature Article
  • Cited 10
  • Views 3,538
  • Annotations
Cite this article as: eLife 2018;7:e31955 doi: 10.7554/eLife.31955

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.

Article and author information

Author details

  1. Gita Mahmoudabadi

    Department of Bioengineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8812-7246
  2. 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.
    ORCID icon "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.

Reviewing Editor

  1. Arup K Chakraborty, Massachusetts Institute of Technology, United States

Publication history

  1. Received: September 17, 2017
  2. Accepted: March 30, 2018
  3. Accepted Manuscript published: April 6, 2018 (version 1)
  4. Version of Record published: April 19, 2018 (version 2)

Copyright

© 2018, Mahmoudabadi & Phillips

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.

Metrics

  • 3,538
    Page views
  • 508
    Downloads
  • 10
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Microbiology and Infectious Disease
    Genevieve S Dobihal et al.
    Research Article
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease
    Guillaume Witz et al.
    Research Article Updated