Dataset: Cyanomyovirus genome sequences

Name: Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America
Published: 2021-06-10
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:48.5005 E:-70.4469 S:32.5593 W:-122.692

Temporal Extent: 2007-08-01 - 2010-09-30

Project:

Cyanophage-Synechococcus interactions in complex communities (Cyanophage-Synechococcus interactions)

Evolutionary ecology of marine cyanophages (Cyanophage Evolutionary Ecology)

Principal Investigator:

Jennifer B.H. Martiny (University of California-Irvine, UC Irvine)

Co-Principal Investigator:

Marcia Marston (Roger Williams University, RWU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-06-10

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/658729/data

Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America

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Description

Cyanomyovirus auxiliary metabolic genome accessions at NCBI GenBank with links to accessions pages.

Related Dataset:
Cyanophage abundance: includes physical data and nutrients from samples collection sites

Acquisition Description

Cyanomyoviruses were isolated on Synechococcus 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).

Plaque-purified isolates were removed from 4°C storage and regrown on Synechococcus 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.

Related references:

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.

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.

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.

Processing Description

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. 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.

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- created links to NCBI accession pages
- added lat, lon, and site name

BCO-DMO data manager processing notes

* Version 2 (2021-06-10) replaces version 1 (2016-10-24). There was an unsupported character in the source file after accession URLs in the hyperlinks. Converted to utf-8 which resolved the problem.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1332782
NSF Division of Ocean Sciences	OCE-1029684
NSF Division of Ocean Sciences	OCE-1332740
NSF Division of Ocean Sciences	OCE-1031783

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
lab_UCIrvine_Martiny		2007-11-15	Unknown Platform	Jennifer B.H. Martiny (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied 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 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
viral_isolate_name	viral isolate identification	unitless	taxon
Genbank_accession	NCBI GenBank accession number	unitless	accession_number
site_code	collection site code	unitless	site
site_name	collection site name	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
isolation_date	isolation date	month-year	date

Database

Geospatial Access

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Dataset: Cyanomyovirus genome sequences