Dataset: Groundwater microorganism retroelement protein sequences
Deployment: Valentine_IFRC_site

Protein sequences from diversity-generating retroelements in groundwater microorganisms

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)

Project:

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

Version:

Data URL:

https://www.bco-dmo.org/dataset-deployment/692460/data

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

Dataset acquisition description

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

Dataset Processing Description

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

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1046144	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2000

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
file_name	Filename	unitless	file_name
description	File description	unitless	brief_desc
file_link	Link to download the data file	unitless	file_link

Database

Contribute Data

Dataset: Groundwater microorganism retroelement protein sequences
Deployment: Valentine_IFRC_site

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Groundwater microorganism retroelement protein sequencesDeployment: Valentine_IFRC_site

Dataset acquisition description

Dataset Processing Description

Dataset: Groundwater microorganism retroelement protein sequences
Deployment: Valentine_IFRC_site