http://lod.bco-dmo.org/id/dataset/632784
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-01-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected on R/V Thomas G. Thompson and R/V Kilo Moana cruises TN232 and KM1005 in the Mariana arc of the western Pacific in 2009 and 2010
2016-01-18
publication
2016-01-18
revision
BCO-DMO Linked Data URI
2016-01-18
creation
http://lod.bco-dmo.org/id/dataset/632784
Julie Huber
Marine Biological Laboratory
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Huber, J. (2016) Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected on R/V Thomas G. Thompson and R/V Kilo Moana cruises TN232 and KM1005 in the Mariana arc of the western Pacific in 2009 and 2010. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 18 Jan 2016) Version Date 2016-01-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/632784 [access date]
Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected in 2009 and 2010. Dataset Description: <p>Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected in 2009 and 2010 on cruises TN232 and KM1005.</p> Methods and Sampling: <p>Diffuse hydrothermal vent fluids were collected at several vent sites on NW Rota-1 seamount in 2009 and 2010 using the ROV Jason 2 and the hydrothermal fluid and particle sampler. Anaerobic enrichment media previously used for the isolation of Caminibacter profundus was inoculated with 1 ml of unfiltered diffuse flow fluids and incubated at 55 degrees&nbsp;C. Enrichments with positive microbial growth were isolated by three sets of dilution-to-extinction. The growth of Lebetimonas under varying conditions including alternative electron donor/acceptor pairs and with N2 gas as the sole nitrogen source was evaluated as described in the Supplementary Material of Meyer &amp; Huber (2014). Growth of Lebetimonas strain JH369 with N2 gas as the sole nitrogen source was evaluated using anaerobic seawater media without yeast extract or ammonia and containing formate and elemental sulfur with an 80% N2 and 20% CO2 headspace.</p>
<p>Genomic DNA was extracted from pure cultures at log phase using a CTAB extraction. Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina). In the case of strains sequenced with multiple platforms, the same genomic DNA extraction was used for all library preparations, with the exception of strain JS085. Genomes were assembled using several tools as described in the Supplementary material of Meyer and Huber 2014.</p>
<p>Related references:<br />
Meyer, J.L. and J.A. Huber. 2014. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME Journal. 8:867–880. doi:<a href="http://dx.doi.org/10.1038/ismej.2013.206" target="_blank">10.1038/ismej.2013.206</a></p>
completed
Julie Huber
Marine Biological Laboratory
(508) 289-2556
Woods Hole Oceanographic Institution Marine Chemistry & Geochemistry, Watson Building, MS51
Woods Hole
MA
02543
USA
jhuber@whoi.edu
pointOfContact
asNeeded
Dataset Version: 18 Jan 2016
Unknown
sequencing_center
domain
phylum
class
order
family
genus
study_name
sample_name
taxon_oid
species
NCBI_accession_num
accession_url
IMG_genome_ID
NCBI_taxon_ID
IMG_submission_ID
GOLD_study_ID
GOLD_study_url
GOLD_project_ID
GOLD_project_url
GOLD_analysis_project_ID
GOLD_analysis_project_url
GOLD_analysis_project_type
gene_model_QC
submission_type
strain
is_public
high_quality
add_date
biotic_relationships
cell_shape
contact_email
contact_name
culture_type
cultured
depth
ecosystem
ecosystem_category
ecosystem_subtype
ecosystem_type
energy_source
GOLD_sequencing_strategy
gram_staining
habitat
isolation
lat
longhurst_code
longhurst_descrip
lon
motility
O2_requirement
project_name
relevance
sporulation
temp_range
gene_count
Jason 2
theme
None, User defined
No BCO-DMO term
phylum
taxonomic class
order
family
genus
species scientific name (binomial)
depth
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
ROV Jason
instrument
BCO-DMO Standard Instruments
TN232
KM1005
service
Deployment Activity
Mariana arc of the western Pacific
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Functional gene diversity and expression in ocean crust microbial communities
https://osprey.bco-dmo.org/project/637566
Functional gene diversity and expression in ocean crust microbial communities
<p><em>Project description from <a href="http://www.darkenergybiosphere.org/education/postdocsFunded.html" target="_blank">C-DEBI</a>:</em><br />
The objective of this project is to determine the diversity, phylogeny, and expression of functional genes involved in carbon, hydrogen, and sulfur cycling in North Pond crustal fluids. These formation fluids are expected to be representative of the ubiquitous cold ocean crust habitat, where reactions between the water and mineral rock surfaces create substrates suitable for sustaining a potentially large reservoir of microbial life. Information regarding crustal microbial communities and the energy sources available for microbial metabolism has been limited by the inaccessibility of samples. IODP Expedition 336 will provide a unique opportunity to access deep subsurface formation fluids from North Pond, including sampling from multiple depth horizons within oceanic crust. My goal is to develop quantitative polymerase chain reaction assays to determine the expression of functional genes in order to increase our understanding of microbial metabolisms in deep subsurface environments.</p>
<p>This project was funded by a C-DEBI Postdoctoral Fellowship to Julie Meyer (formerly at the Marine Biological Laboratory).</p>
NP Functional Gene Div
largerWorkCitation
project
eng; USA
biota
oceans
Mariana arc of the western Pacific
2016-01-18
North Pond
0
BCO-DMO catalogue of parameters from Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected on R/V Thomas G. Thompson and R/V Kilo Moana cruises TN232 and KM1005 in the Mariana arc of the western Pacific in 2009 and 2010
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/635873.rdf
Name: sequencing_center
Units: dimensionless
Description: <p>Name of sequencing center.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635874.rdf
Name: domain
Units: dimensionless
Description: <p>Domain of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635875.rdf
Name: phylum
Units: dimensionless
Description: <p>Taxonomic phylum.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635876.rdf
Name: class
Units: dimensionless
Description: <p>Taxonomic class.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635877.rdf
Name: order
Units: dimensionless
Description: <p>Taxonomic order.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635878.rdf
Name: family
Units: dimensionless
Description: <p>Taxonomic family.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635879.rdf
Name: genus
Units: dimensionless
Description: <p>Taxonomic genus.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635880.rdf
Name: study_name
Units: dimensionless
Description: <p>Name of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635881.rdf
Name: sample_name
Units: dimensionless
Description: <p>Name/identifier of the sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635882.rdf
Name: taxon_oid
Units: dimensionless
Description: <p>Taxon identier (OID).</p>
http://lod.bco-dmo.org/id/dataset-parameter/635883.rdf
Name: species
Units: dimensionless
Description: <p>Species identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635884.rdf
Name: NCBI_accession_num
Units: dimensionless
Description: <p>NCBI accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635885.rdf
Name: accession_url
Units: dimensionless
Description: <p>Hyperlink to NCBI for the accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635886.rdf
Name: IMG_genome_ID
Units: dimensionless
Description: <p>IMG database (<a href="http://img.jgi.doe.gov/">http://img.jgi.doe.gov/</a>) genome identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635887.rdf
Name: NCBI_taxon_ID
Units: dimensionless
Description: <p>NCBI taxon identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635888.rdf
Name: IMG_submission_ID
Units: dimensionless
Description: <p>IMG database (<a href="http://img.jgi.doe.gov/">http://img.jgi.doe.gov/</a>) submission identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635889.rdf
Name: GOLD_study_ID
Units: dimensionless
Description: <p>GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) study identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635890.rdf
Name: GOLD_study_url
Units: dimensionless
Description: <p>Hyperlink to GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) for the study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635891.rdf
Name: GOLD_project_ID
Units: dimensionless
Description: <p>GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) project identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635892.rdf
Name: GOLD_project_url
Units: dimensionless
Description: <p>Hyperlink to GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) for the project.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635893.rdf
Name: GOLD_analysis_project_ID
Units: dimensionless
Description: <p>GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) analysis project identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635894.rdf
Name: GOLD_analysis_project_url
Units: dimensionless
Description: <p>Hyperlink to GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) for the analysis project identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635895.rdf
Name: GOLD_analysis_project_type
Units: dimensionless
Description: <p>GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) project type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635896.rdf
Name: gene_model_QC
Units: dimensionless
Description: <p>Gene model QC? (yes/no)</p>
http://lod.bco-dmo.org/id/dataset-parameter/635897.rdf
Name: submission_type
Units: dimensionless
Description: <p>Submission type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635898.rdf
Name: strain
Units: dimensionless
Description: <p>Strain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635899.rdf
Name: is_public
Units: dimensionless
Description: <p>Is the dataset public? (yes/no)</p>
http://lod.bco-dmo.org/id/dataset-parameter/635900.rdf
Name: high_quality
Units: dimensionless
Description: <p>Is it a high quality dataset? (yes/no)</p>
http://lod.bco-dmo.org/id/dataset-parameter/635901.rdf
Name: add_date
Units: dimensionless
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/635902.rdf
Name: biotic_relationships
Units: dimensionless
Description: <p>Description of the biotic relationships.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635903.rdf
Name: cell_shape
Units: dimensionless
Description: <p>Description of the cell shape.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635904.rdf
Name: contact_email
Units: dimensionless
Description: <p>Contact email address.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635905.rdf
Name: contact_name
Units: dimensionless
Description: <p>Contact name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635906.rdf
Name: culture_type
Units: dimensionless
Description: <p>Culture type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635907.rdf
Name: cultured
Units: dimensionless
Description: <p>Cultured? (yes/no)</p>
http://lod.bco-dmo.org/id/dataset-parameter/635908.rdf
Name: depth
Units: dimensionless
Description: <p>Depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635909.rdf
Name: ecosystem
Units: dimensionless
Description: <p>Description of ecosystem.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635910.rdf
Name: ecosystem_category
Units: dimensionless
Description: <p>Description of ecosystem category.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635911.rdf
Name: ecosystem_subtype
Units: dimensionless
Description: <p>Description of ecosystem sub-type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635912.rdf
Name: ecosystem_type
Units: dimensionless
Description: <p>Description of ecosystem type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635913.rdf
Name: energy_source
Units: dimensionless
Description: <p>Energy source.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635914.rdf
Name: GOLD_sequencing_strategy
Units: dimensionless
Description: <p>GOLD database (<a href="https://gold.jgi.doe.gov/">https://gold.jgi.doe.gov/</a>) sequencing strategy.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635915.rdf
Name: gram_staining
Units: dimensionless
Description: <p>Type of gram staining.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635916.rdf
Name: habitat
Units: dimensionless
Description: <p>Description of habitat.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635917.rdf
Name: isolation
Units: dimensionless
Description: <p>Description of isolation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635918.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635919.rdf
Name: longhurst_code
Units: dimensionless
Description: <p>Longhurst code.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635920.rdf
Name: longhurst_descrip
Units: dimensionless
Description: <p>Longhurst description.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635921.rdf
Name: lon
Units: decimal degress
Description: <p>Longitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635922.rdf
Name: motility
Units: dimensionless
Description: <p>Motility.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635923.rdf
Name: O2_requirement
Units: dimensionless
Description: <p>O2 requirements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635924.rdf
Name: project_name
Units: dimensionless
Description: <p>Project name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635925.rdf
Name: relevance
Units: dimensionless
Description: <p>Relevance.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635926.rdf
Name: sporulation
Units: dimensionless
Description: <p>Type of sporulation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635927.rdf
Name: temp_range
Units: dimensionless
Description: <p>Description of temperature range.</p>
http://lod.bco-dmo.org/id/dataset-parameter/635928.rdf
Name: gene_count
Units: dimensionless
Description: <p>Gene count.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
7874
https://datadocs.bco-dmo.org/file/g77yqvlcNGQZZD/Lebetimonas_genomes.csv
Lebetimonas_genomes.csv
Primary data file for dataset ID 632784
download
https://osprey.bco-dmo.org/dataset/632784/data/download
download
onLine
dataset
<p>Diffuse hydrothermal vent fluids were collected at several vent sites on NW Rota-1 seamount in 2009 and 2010 using the ROV Jason 2 and the hydrothermal fluid and particle sampler. Anaerobic enrichment media previously used for the isolation of Caminibacter profundus was inoculated with 1 ml of unfiltered diffuse flow fluids and incubated at 55 degrees&nbsp;C. Enrichments with positive microbial growth were isolated by three sets of dilution-to-extinction. The growth of Lebetimonas under varying conditions including alternative electron donor/acceptor pairs and with N2 gas as the sole nitrogen source was evaluated as described in the Supplementary Material of Meyer &amp; Huber (2014). Growth of Lebetimonas strain JH369 with N2 gas as the sole nitrogen source was evaluated using anaerobic seawater media without yeast extract or ammonia and containing formate and elemental sulfur with an 80% N2 and 20% CO2 headspace.</p>
<p>Genomic DNA was extracted from pure cultures at log phase using a CTAB extraction. Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina). In the case of strains sequenced with multiple platforms, the same genomic DNA extraction was used for all library preparations, with the exception of strain JS085. Genomes were assembled using several tools as described in the Supplementary material of Meyer and Huber 2014.</p>
<p>Related references:<br />
Meyer, J.L. and J.A. Huber. 2014. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME Journal. 8:867–880. doi:<a href="http://dx.doi.org/10.1038/ismej.2013.206" target="_blank">10.1038/ismej.2013.206</a></p>
Specified by the Principal Investigator(s)
<p>Prior to assembly, Illumina sequences were quality filtered using adaptive window trimming and a quality threshold of 30 using the script Trim.pl (<a href="http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.pl" target="_blank">http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.pl</a>). All reads were screened for adaptor, barcorde, primer, and transposan sequences and trimmed as needed using FASTX-Toolkit (<a href="http://hannonlab.cshl.edu/fastx_toolkit/index.html" target="_blank">http://hannonlab.cshl.edu/fastx_toolkit/index.html</a>). De novo genome assembly was performed with several assembly programs. Sequences generated through the 454 platform were first assembled with Roche’s GS De Novo Assembler v 2.6 ("Newbler") 2 using default parameters. De novo assemblies of 454 reads were also performed using mira 3 with the default settings for normal quality de novo genome assembly. De novo assembly of subsets of Illumina reads was performed with velvet 4, using an estimated coverage of 1000x, kmer size of 21, and a coverage cutoff of 5). Large contigs from Newbler , mira, and velvet were consolidated using Geneious Pro v 5.6.6 (Biomatters, Ltd, http://www.geneious.com) and aligned with progressiveMauve 5 to visualize the relationship of large contigs from different assemblies and to identify gaps to close. Primers were designed at the ends of contigs using either Geneious Pro or CLC Genomics Workbench v 5.1 (CLCbio, <a href="http://www.clcbio.com" target="_blank">http://www.clcbio.com</a>) to amplify gaps between contigs. Positive PCR amplification products linking contigs were cleaned using a Min-Elute PCR Purification kit (Qiagen) and Sanger sequenced. A nearly complete draft genome from strain JS085 served as a reference genome for the remaining five strains. Both Illumina and 454 reads were mapped to the reference genome with CLC Genomics Workbench. Unmapped reads were then assembled de novo to ensure that novel genomic content in the mapped strains was not overlooked. De novo assembly of 454 and/or Illumina reads for each strain was also performed in CLC Genomics Workbench and compared to the mapped assemblies using progressiveMauve.</p>
<p>Four of the strains were sequenced using both 454 and Illumina and two strains were sequenced only with Illumina. The sequencing coverage depth of quality-filtered reads ranged from 22X to 50X for 454 and up to 3618X for Illumina. Lebetimonas strain JS085 had the highest coverage of 454 reads and was assembled into 33 large contigs with Newbler and 1747 contigs with mira. The 20 largest contigs from each of these assemblies were consolidated using de novo assembly in Geneious to 10 contigs. An additional round of assembly in Geneious with the 10 consolidated contigs and velvet contigs greater than 10 Kbp further consolidated the draft genome to 6 contigs. Primers were designed for all possible combinations between the 6 contigs. One gap was closed using Sanger-sequenced positive pcr products. Finally, all 454 and Illumina reads for strain JS085 were mapped to the draft genome consisting of 5 contigs and the resulting consensus was used as the final draft genome. The five remaining genomes were assembled by mapping 454 and Illumina reads to the JS085 reference genome in CLC Genomics Workbench. Hybrid de novo assemblies in CLC Genomics Workbench of each strain did not extend contigs or close gaps between the 5 contigs of the draft genomes. Assemblies of unmapped reads produced only short contigs with no significant similarities using nucleotide BLAST 6.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- added hyperlinks;<br />
- removed "m" (meters) in depth column.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: PI Supplied Instrument Description:Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Jason 2
Jason 2
PI Supplied Instrument Name: Jason 2 Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument Description: The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/
Cruise: TN232
TN232
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN232
William Chadwick
National Oceanic and Atmospheric Administration
Cruise: KM1005
KM1005
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1005
William Chadwick
National Oceanic and Atmospheric Administration
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel