The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology
Open accessAbstract
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,587
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,491
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · cited 2×
“To study this ‘unseen majority’ [13], microbial ecologists developed culture-independent techniques, first in the form of gene markers (e.”
BackgroundEnvironmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,701
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
The Microbial Engines That Drive Earth's Biogeochemical Cycles
Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008) · Science · doi:10.1126/science.1153213 · Cited by 3,379
A Molecular View of Microbial Diversity and the Biosphere
Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,746
Metagenomics: Application of Genomics to Uncultured Microorganisms
Handelsman, J. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.4.669-685.2004 · Cited by 2,441
Cited by
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Steinegger, M., & Söding, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3988 · Cited by 4,840
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B. (2015) · eLife · doi:10.7554/elife.08490 · Cited by 478
Self-citationBikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., Del Pozo-Yauner, L., & Ochoa-Leyva, A. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.06.001 · Cited by 263
Unifying the known and unknown microbial coding sequence space
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife · doi:10.7554/elife.67667 · Cited by 134
Metadata
- Authors
- Hurwitz, B. L., & Sullivan, M. B.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-02-28
- Volume
- 8
- Issue
- 2
- Pages
- e57355
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2074955520
- Cited by
- 334
- References
- 70
- FWCI
- 32.52
- Type
- journal article
- Language
- en
- Open access
- gold
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