Dataset: Groundwater microorganism retroelement protein sequences

Name: Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project)
Published: 2017-04-11
Keywords: oceans

Cite This Dataset

Spatial Extent: N:39.5291 E:-107.7721 S:39.5291 W:-107.7721

Project:

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

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

David L. Valentine (University of California-Santa Barbara, UCSB)

Student:

Blair Paul (University of California-Santa Barbara, UCSB-MSI)

Contact:

David L. Valentine (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-04-11

Restricted:

Validated:

Current State:

Final no updates expected

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

Expand/Collapse All

Description

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

Methods & Sampling

A bioinformatic analysis of metagenome-assembled genomes to identify retroelements was performed. This study used data from several previously described sampling efforts (Brown et al. 2015, Castelle et al. 2015, and Anantharaman et al. 2016). Original sampling was conducted within an unconfined aquifer at the Rifle Integrated Field Research Challenge (IFRC) site, which is adjacent to the Colorado River, near Rifle, Colorado, USA (39.5291, -107.7721). Samples were collected between August 25th to December 12th of 2011, and August 2nd to December 12th of 2012. Sequencing of these samples took place at the Joint Genome Institute using the Illumina HiSeq 2000 platform to generate 2 × 150 paired-end reads.

For more information about sampling methodology see Paul et al. 2017.

Data Processing Description

These sequences were processed using Python v2.7.12, and Geneious v8.1.4.

Data Files