Dataset: Nitrosopelagicus brevis genome

Name: NCBI Accession number link to the closed genome of Nitrosopelagicus brevis CN25 (AmoA Archaea project)
Published: 2016-10-13
Keywords: archea, genome, biota, oceans

Cite This Dataset

Project:

Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea (AmoA Archaea)

Principal Investigator:

Alyson E. Santoro (University of California-Santa Barbara, UCSB)

Co-Principal Investigator:

Christopher Dupont (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

2016.05.06

Version Date:

2016-10-13

Restricted:

Validated:

Yes

Current State:

Final with updates expected

Data URL:

https://www.bco-dmo.org/dataset/661548/data

NCBI Accession number link to the closed genome of Nitrosopelagicus brevis CN25 (AmoA Archaea project)

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Description

The closed genome of Nitrosopelagicus brevis CN25.

The sequence reported here has been deposited in the GenBank database (accession no. CP007026).

Related publication:

Santoro AE et al.,"Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean.", Proc Natl Acad Sci U S A, 2015 Jan 13;112(4):1173-8. doi: 10.1073/pnas.1416223112 (link to corresponding pubmed entry at NCBI)

Methods & Sampling

Illumina sequencing of an enrichment metagenome of a marine thaumarcheota culture.

Data Processing Description

The Celera assembler was used for genome assembly, with binning based on coverage. Seven initial contigs were closed into a circular chromosome using manual alignments, PCR gap bridging, and Sanger. Gene calls and annotations were conducted with the JCVI Prokaryotic Genome Annotation pipeline.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1259994
NSF Division of Ocean Sciences	OCE-1260006

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: illumina sequencer

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
accession no.	NCBI Accession number.	unitless	accession_number

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Database

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Dataset: Nitrosopelagicus brevis genome