A single drop of seawater contains between a million and fifty million free virus particles, making viruses the most abundant biological entity in the oceans. Viruses affect all life in the oceans, especially microorganisms like the single-celled algae and bacteria at the base of the marine food web. Because microorganisms are critical to the health and productivity of marine ecosystems, any process that impacts microbial activity may have a larger, secondary impact on marine ecosystems. Although they are minutely small—a ten-millionth of a meter in diameter—viruses can have a large impact on ecosystems by infecting and lysing microbial cells. While scientists are beginning to appreciate the larger scale impacts of viruses on marine ecosystems, they know little about the details of how viruses affect individual groups of microorganisms. These smaller details are critical to understanding how viruses may influence the growth and activity of important microbial groups within the ocean. Through DNA sequencing, scientists now have a tool for uncovering detailed information about viruses in the ocean. The goal of our project is to develop easy-to-use software that runs in a web browser and allows biologists with little computer training to explore detailed genetic information about viruses within the ocean.
A central challenge in analyzing shotgun viral metagenome sequence data comes through the fact that only a small proportion — 10 to 25% — of sequences within a typical viral metagenome (or viral genome) show homology to a gene of known function. This fact has been the driving motivation behind our development of a bioinformatics pipeline and web-application interface known as the Viral Informatics Resource fOr Metagenome Exploration (VIROME; virome.dbi.udel.edu). The uniting analytical feature of VIROME is the classification of each predicted open reading frame (ORF, an operational definition for a gene) into one of nine sequence categories depending on the nature of its top sequence homolog: two classes are structural RNAs; two relate to genes with possible functional assignments; four classes of environmental proteins; and true ORFans, sequences showing no significant homology to any other sequence. The Gordon and Betty Moore Foundation has made a substantial investment in the advancement of viral ecology research through its Marine Phage, Viruses and Viromes project at the Broad Institute (www.broadinstitute.org/annotation/viral/Phage/), which has produced genome sequence data from nearly one hundred marine viruses and at least as many viral metagenome samples (viromes). Thus, the central goal of our project is to further scientific understanding of marine viruses by providing researchers involved in the MMI marine virus sequencing project and others access to an easy-to-use web application specifically designed for bioinformatic analysis of viral metagenome sequence data.
Wommack, K. E., Bhavsar J., Polson, S.W., Chen, J., Dumas, M., Srinivasiah, S., Furman M., Jamindar, S., & Nasko, D. J. (2012). VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci, 6(3), 427-439. doi: 10.4056/sigs.2945050
Polson, S. W., S. W. Wilhelm, & K. E. Wommack. (2011). Unraveling the viral tapestry (from inside the capsid out). ISME Journal, 5(2), 165-168. doi: 10.1038/ismej.2010.81
The link to the VIROME web-application resource can be found at: http://virome.dbi.udel.edu/
Videos on the use of VIROME can be found on the following YouTube channel: https://www.youtube.com/user/TeamVIROME
Publications that leverage VIROME:
Sakowski, E. G., Munsell, E. V., Hyatt, M., Kress, W., Williamson, S. J., Nasko, D. J., Polson, S. W., & Wommack, K.E. (2014). Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses PNAS 111(44), 15786-15791. doi: 10.1073/pnas.1401322111
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