http://lod.bco-dmo.org/id/dataset/658729
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
2016-09-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America
2021-06-10
publication
2021-06-10
revision
BCO-DMO Linked Data URI
2021-06-10
creation
http://lod.bco-dmo.org/id/dataset/658729
Jennifer B.H. Martiny
University of California-Irvine
principalInvestigator
Marcia Marston
Roger Williams University
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: Martiny, J. B., Marston, M. (2021) Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/658729 [access date]
Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America Dataset Description: <p>Cyanomyovirus auxiliary metabolic genome accessions at NCBI GenBank with links to accessions pages.</p>
<p><strong>Related Dataset:</strong><br />
<a href="http://www.bco-dmo.org/dataset/3507" target="_blank">Cyanophage abundance</a>: includes physical data and nutrients from samples collection sites</p> Methods and Sampling: <p>Cyanomyoviruses were isolated on <em>Synechococcus</em> sp. WH7803 or WH8101 from surface seawater samples collected from Southern California (n=19) between 2008 and 2010; Padilla Bay, Washington (n=3) in August 2010; and Narragansett Bay, Rhode Island (n=108) from 1999 to 2015 as described in Clasen et al. (2013) and Marston et al. (2013).</p>
<p>Plaque-purified isolates were removed from 4<strong>°</strong>C storage and regrown on <em>Synechococcus</em> sp. WH7803 liquid culture. Phage genomic DNA was extracted as described in Henn et al. (2010). A genomic DNA library was prepared for Illumina sequencing as described in the “Low Sample (LS) Protocol” of the Illumina TruSeq DNA sample prep kit. Samples were sequenced on an Illumina HiSeq2000 sequencer (single read, paired-end with 100 cycles) at the UCI Genomics High-throughput Facility or on a Illumina MiSeq at the Rhode Island Genomics and Sequencing Center at the University of Rhode Island.</p>
<p><strong>Related references:&nbsp; </strong></p>
<p>Clasen, J., Hanson, C., Ibrahim, Y., Weihe, C., Marston, M., Martiny, J., 2013. Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates. Aquat Microb Ecol 69, 17-31.</p>
<p>Henn, M.R., Sullivan, M.B., Stange-Thomann, N., Osburne, M.S., Berlin, A.M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S.K., Nusbaum, C., Birren, B.W., Chisholm, S.W., 2010. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS ONE 5, e9083.</p>
<p>Marston, M. F., Taylor, S., Sme, N., Parsons, R., Noyes, T. J. E., and Martiny, J. B. H. (2013). Marine cyanophages exhibit local and regional biogeography. Environ. Microbiol. 15, 452–1463. doi: 10.1111/1462-2920.12062.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1031783 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1031783
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029684 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029684
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332740 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332740
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332782 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332782
completed
Jennifer B.H. Martiny
University of California-Irvine
949-824-0487
Dept. of Ecology and Evolutionary Biology 321 Steinhaus Hall
Irvine
CA
92697-2525
USA
jmartiny@uci.edu
pointOfContact
Marcia Marston
Roger Williams University
401-254-3673
Department of Biology 1 Old Ferry Road
Bristol
RI
02809
USA
mmarston@rwu.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
viral_isolate_name
Genbank_accession
site_code
site_name
lat
lon
isolation_date
theme
None, User defined
taxon
accession number
site
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
lab_UCIrvine_Martiny
service
Deployment Activity
Southern California
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.
Evolutionary ecology of marine cyanophages
http://jmartiny.bio.uci.edu/
Evolutionary ecology of marine cyanophages
<p> ABSTRACT</p>
<p>The evolutionary ecology of virus-host interactions are key to understanding viral-induced mortality rates in marine ecosystems, as the pattern and dynamics of virus-host interactions will ultimately determine the influence of viruses on nutrient cycling. Recent studies suggest that the diversity and composition of marine viruses appears to vary over time and space. The goal of this research is to move beyond simply documenting biogeographic patterns in marine viruses and to begin to ask why the genetic composition of marine viruses varies over time and space. Part of the challenge in doing this is that little is known about how the genetic diversity of a marine virus relates to its phenotype. To address this challenge, the PIs are taking an isolation approach, using lytic cyanophages that infect marine <em>Synechococcus</em> as a model system. In this way they can compare the genotype and phenotype of each virus isolate.</p>
<p>There are three specific goals to do this: (1) Identify genetic markers of cyanophage host range (the particular hosts that a phage can infect); (2) Conduct a time-series study of cyanophage isolates from the Pacific and Atlantic coasts of North America; and (3) Using isolates from the time series, characterize cyanophage phenotypes.</p>
<p><strong>Relevant References:</strong></p>
<p>Marston, M., S. Taylor, N. Sme, R. Parsons, T. Noyes, J.B.H. Martiny. "Marine cyanophages exhibit local and regional biogeography," Environmental Microbiology, v.15, 2013, p. 1452.</p>
<p>Clasen J.L.*, C.A. Hanson*, Y. Ibrahim, C. Weihe, M.F. Marston, and J.B.H. Martiny. "Diversity and temporal dynamics of southern California coastal marine cyanophage isolates," Aquatic Microbial Ecology, v.69, 2013, p. 17.</p>
<p>Marston, M.F., F.J. Pierciey, A. Shepard, G. Gearin, J. Qi, C. Yandava, S.C. Schuster, M.R. Henn, J.B.H. Martiny. "Rapid diversification of coevolving marine Synechococcus and a virus," Proceedings of the National Academy of Sciences, v.109, 2012, p. 4544.</p>
<p>Hanson, C.A., J.A. Fuhrman, M.C. Horner-Devine, J.B.H. Martiny. "Beyond biogeographic patterns: processes shaping the microbial landscape," Nature Reviews Microbiology, v.10, 2012, p. 497.</p>
Cyanophage Evolutionary Ecology
largerWorkCitation
project
Cyanophage-Synechococcus interactions in complex communities
https://osprey.bco-dmo.org/project/529066
Cyanophage-Synechococcus interactions in complex communities
<p><em>Description from NSF award abstract:</em><br />
Viral-induced mortality of marine microorganisms alters the quantity and quality of pools of dissolved organic matter in the oceans, shuttling organic matter back into the microbial loop and away from the larger marine food web. A major hindrance to understanding the role of viruses in biogeochemical cycling is that we know surprisingly little about which viruses infect which bacteria in the marine environment. In this project, a network-based framework will be used to investigate marine phage-bacteria interactions in complex, multispecies communities. The research focuses on cyanophages, viruses that infect Synechococcus, an ecologically important cyanobacterium in the oceans. There are three parts of the project. The first part will identify genetic signatures of cyanophage-Synechococcus interactions by using laboratory evolution experiments and genomic sequencing. The second part will examine the temporal and spatial diversity of these candidate interaction genes in natural cyanophage populations, by comparing the full genome sequences of hundreds of isolates previously collected over many years. The third part will adapt the new method of viral-tagging to natural host populations to characterize cyanophage-Synechococcus interaction networks in the environment.</p>
<p>The role of viruses in global marine biogeochemical cycles depends on viral-induced mortality rates, which have been estimated to vary widely. The pattern and dynamics of who infects whom are central to our understanding of these rates as well as the role viruses play in marine nutrient cycling. This project will also contribute generally to our knowledge about viral diversity. The vast majority of marine viral sequences are not similar to any known diversity, and it is reasonable to conclude that many of these genes have to do with host recognition and infection. Finally, this project will develop a method of characterizing phage-bacteria interactions in natural, diverse microbial communities, thereby opening avenues for similar studies of viruses in other environments.</p>
<p>Note: This is an NSF Collaborative Research Project supported by OCE-1332740 (Lead PI Jennifer Martiny) and OCE-1332782 (Lead PI Marica Marston).</p>
Cyanophage-Synechococcus interactions
largerWorkCitation
project
eng; USA
biota
oceans
Southern California
-122.692
-70.4469
32.5593
48.5005
2007-08-01
2010-09-30
From projects that focused on the following 2 locations: 1. Pacific and Atlantic coasts of North America 2. coastal locations in CA and RI
0
BCO-DMO catalogue of parameters from Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America
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/658737.rdf
Name: viral_isolate_name
Units: unitless
Description: <p>viral isolate identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/658738.rdf
Name: Genbank_accession
Units: unitless
Description: <p>NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658739.rdf
Name: site_code
Units: unitless
Description: <p>collection site code</p>
http://lod.bco-dmo.org/id/dataset-parameter/658740.rdf
Name: site_name
Units: unitless
Description: <p>collection site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/658741.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658742.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658743.rdf
Name: isolation_date
Units: month-year
Description: <p>isolation date</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
22627
https://datadocs.bco-dmo.org/file/m77kmREFWZE2wA/cyanomyovirus_access.csv
cyanomyovirus_access.csv
Primary data file for dataset ID 658729
download
https://osprey.bco-dmo.org/dataset/658729/data/download
download
onLine
dataset
<p>Cyanomyoviruses were isolated on <em>Synechococcus</em> sp. WH7803 or WH8101 from surface seawater samples collected from Southern California (n=19) between 2008 and 2010; Padilla Bay, Washington (n=3) in August 2010; and Narragansett Bay, Rhode Island (n=108) from 1999 to 2015 as described in Clasen et al. (2013) and Marston et al. (2013).</p>
<p>Plaque-purified isolates were removed from 4<strong>°</strong>C storage and regrown on <em>Synechococcus</em> sp. WH7803 liquid culture. Phage genomic DNA was extracted as described in Henn et al. (2010). A genomic DNA library was prepared for Illumina sequencing as described in the “Low Sample (LS) Protocol” of the Illumina TruSeq DNA sample prep kit. Samples were sequenced on an Illumina HiSeq2000 sequencer (single read, paired-end with 100 cycles) at the UCI Genomics High-throughput Facility or on a Illumina MiSeq at the Rhode Island Genomics and Sequencing Center at the University of Rhode Island.</p>
<p><strong>Related references:&nbsp; </strong></p>
<p>Clasen, J., Hanson, C., Ibrahim, Y., Weihe, C., Marston, M., Martiny, J., 2013. Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates. Aquat Microb Ecol 69, 17-31.</p>
<p>Henn, M.R., Sullivan, M.B., Stange-Thomann, N., Osburne, M.S., Berlin, A.M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S.K., Nusbaum, C., Birren, B.W., Chisholm, S.W., 2010. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS ONE 5, e9083.</p>
<p>Marston, M. F., Taylor, S., Sme, N., Parsons, R., Noyes, T. J. E., and Martiny, J. B. H. (2013). Marine cyanophages exhibit local and regional biogeography. Environ. Microbiol. 15, 452–1463. doi: 10.1111/1462-2920.12062.</p>
Specified by the Principal Investigator(s)
<p>Genome assembly of paired-end reads was performed with CLC Genomics Workbench 6.0.2 software using the default software parameters or with the Geneious software package.&nbsp; Genome coverage (nucleotide redundancy) ranged from 2,000x – 8,000x. ORF calling and primary annotation of protein coding sequences (CDS) and transfer RNAs were performed using RAST.</p>
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- created links to NCBI accession pages<br />
- added lat, lon, and site name<br />
<br />
&nbsp;</p>
<div><span style="font-size:13px">BCO-DMO data manager processing notes</span></div>
<div><span style="font-size:13px">* Version 2 (2021-06-10) replaces version 1 (</span>2016-10-24<span style="font-size:13px">).&nbsp; &nbsp;There was an unsupported character in the source file after accession URLs in the hyperlinks. Converted to utf-8 which resolved the problem.</span></div>
<p><br />
&nbsp;</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:Illumina HiSeq2000 sequencer (single read, paired-end with 100 cycles) at the UCI Genomics High-throughput Facility or Illumina MiSeq at the Rhode Island Genomics and Sequencing Center at the University of Rhode Island. 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.
Deployment: lab_UCIrvine_Martiny
lab_UCIrvine_Martiny
Unknown Platform
lab_UCIrvine_Martiny
Jennifer B.H. Martiny
University of California-Irvine
Unknown Platform