Dataset: Brothers Volcano Metagenome-Assembled Genome Accession Numbers

Name: Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano
Published: 2022-01-19
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.868323.1

Spatial Extent: N:-34.8579131 E:179.071443 S:-34.8823655 W:179.051933

Temporal Extent: 2018-03 - 2018-03

Project:

Collaborative Research: Hydrothermal and Microbiological Investigations of the Active Brothers Volcano in the Kermadec Arc (Brothers Volcano Microbiology)

Principal Investigator:

Anna-Louise Reysenbach (Portland State University, PSU)

Co-Principal Investigator:

Susan Humphris (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-01-19

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano

Abstract:

Accession numbers for metagenome-assembled genomes (MAGs) from the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano. Published in Reysenbach & St. John et al., 2020. Sequence data is available in NCBI Genbank under BioProject accession PRJNA546572.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-01-19	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.868323.1	2022-08-24

Methods & Sampling

Water samples and hydrothermal vent deposits were collected as described in Reysenbach & St. John et al., 2020. Samples were collected with remotely operated vehicle ROV Jason. Water samples were obtained using major water samplers. Hydrothermal deposits were placed in sealed bioboxes in the ROV sampling basket to restrict flushing of samples by surrounding seawater during the ascent. Once shipboard, 1L of water samples were filtered through a 0.2-μm Sterivex filter (Merck). For the hydrothermal deposits, the outer few millimeters (up to approximately 5 mm) was subsampled for DNA extraction. These exterior samples were homogenized and stored in cryovials at -80 degrees C for subsequent DNA extraction. For the water samples, the DNA was extracted from the sterivex filters as previously described by R. E. Anderson et al. (2017). The DNA was extracted from the homogenized hydrothermal depot samples using the DNeasy PowerSoil kit (Qiagen) All purified environmental DNA was stored at -80 degrees C. After DNA extraction and library preparation, metagenomes were sequenced using the Illumina HiSeq 3000.

Data Processing Description

Data Processing:
Metagenome reads were trimmed using Trimmomatic, and assembled into contigs with MEGAHIT. Reads were then mapped back to the contigs with Bowtie2 and SAMtools. Metagenome-assembled genomes were binned using MetaBAT, followed by curation of key genomes using Emergent Self Organizing Maps.

Software:
Trimmomatic v.0.36: Trimming software for read processing.

MEGAHIT v.1.1.1-2-g02102e1: Assembly software used to generate contigs from reads.

Bowtie2 v.2.2.9 and SAMtools v.1.3.1: Software used to map reads back to contigs and parse results of the mapping.

MetaBAT v.0.32.4: Binning software, used to group contigs into metagenome-assembled genomes (MAGs).

Emergent Self Organizing Maps (ESOM): manual binning software used to curate genomes of interest.

BCO-DMO Processing:
- removed commas from Collection_location column;
- removed directional letters from the Latitude and Longitude columns and made Latitude values negative to indicate South;
- converted Collection_date field to YYYY-MM format.

Data Files

File
accessions.csv (Comma Separated Values (.csv), 127.20 KB) MD5:daaeddac8c48edc050062d9bfa67034c Primary data file for dataset ID 868323

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1558356
NSF Division of Ocean Sciences	OCE-1558795

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN350		2018-03-03	R/V Thomas G. Thompson	Anna-Louise Reysenbach (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 3000

Supplied Description:

Illumina HiSeq 3000: Sequencing platform used to generate metagenome reads

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
Sample	Sample identifier	unitless	sample
MAG	Metagenome-assembled genome (MAG) identifier	unitless	sample
Repository	Public database where data is deposited	unitless	no_bcodmo_term
Biosample_accession	Genbank Biosample accession number	unitless	BioSample
WGS_accession	Genbank whole genome sequence accession number	unitless	accession_number
Organism	Genbank-compatable organism name	unitless	taxon
Collection_location	Geographic location of collection	unitless	site
Collection_date	Collection date; format: YYYY-MM Format: %Y-%m	unitless	date
Latitude	Collection latitude	decimal degrees North	lat
Longitude	Collection longitude	decimal degrees East	lon
Depth	Depth	meters	depth
Sequencing_technology	Technology used to sequence metagenomes	unitless	instrument
Assembly_program	Software used to assemble contigs from metagenome reads	unitless	sampling_method
Binning_program	Software used to bin MAGs from contigs	unitless	sampling_method

Status message

Database

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Dataset: Brothers Volcano Metagenome-Assembled Genome Accession Numbers