Dataset: Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project)

This dataset has not been validatedFinal no updates expectedVersion 1 (2017-04-11)Dataset Type:experimental

Principal Investigator, Contact: David L. Valentine (University of California-Santa Barbara)

Student: Blair Paul (University of California-Santa Barbara)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Program: Dimensions of Biodiversity (Dimensions of Biodiversity)

Project: Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems (Viruses in Methanotrophic Marine Ecosystems)

Cite Dataset

This dataset includes links to diversity-generating retroelement sequences files in .fasta format.  There are separate .fasta files for reverse transcriptase protein sequences and variable protein sequences.  These sequences were derived from previously generated sequence accessions at the National Center for Biotechnology Information (NCBI).  Original sampling took place near Rifle, Colorado​ between 2011 and 2012.

To access the .fasta files and the list of source sequences, click the "Get Data" button at the top of this page.

These data are published in the following journal article:
Paul, B.G., Burstein, D., Castelle, C.J., Handa, S., Arambula, D., Czornyj, E., Thomas, B.C., Ghosh, P., Miller, J.F., Banfield, J.F. and Valentine, D.L. (2017) Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nature Microbiology, 2, p.17045. doi: 10.1038/nmicrobiol.2017.45

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Related Publications

Methods, Results
Paul, B. G., Burstein, D., Castelle, C. J., Handa, S., Arambula, D., Czornyj, E., … Valentine, D. L. (2017). Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nature Microbiology, 2, 17045. doi:10.1038/nmicrobiol.2017.45
Methods
Anantharaman, K., Brown, C. T., Hug, L. A., Sharon, I., Castelle, C. J., Probst, A. J., … Banfield, J. F. (2016). Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications, 7, 13219. doi:10.1038/ncomms13219
Methods
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., … Banfield, J. F. (2015). Unusual biology across a group comprising more than 15% of domain Bacteria. Nature, 523(7559), 208–211. doi:10.1038/nature14486
Methods
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., … Banfield, J. F. (2015). Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling. Current Biology, 25(6), 690–701. doi:10.1016/j.cub.2015.01.014

Valentine, D. L. (2017) Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-04-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/687822 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation