Dataset: sea_fan_parasite_sequences

Name: Accession numbers for Labyrinthulomycetes detected in sea fans collected in the Florida Keys and Puerto Rico from 2006-2010 (Climate_CoralDisease project)
Published: 2012-09-12
Keywords: oceans

Cite This Dataset

Spatial Extent: N:24.5535 E:-67.0489 S:17.9349 W:-81.3789

Project:

Influence of Temperature and Acidification on the Dynamics of Coral Co-Infection and Resistance (Climate_CoralDisease)

Principal Investigator:

Drew Harvell (Cornell University, Cornell)

Co-Principal Investigator:

Laura Mydlarz (University of Texas at Arlington, UT Arlington)

Contact:

Dr Colleen Burge (Cornell University, Cornell)

BCO-DMO Data Manager:

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

Version:

12 Sept 2012

Version Date:

2012-09-12

Validated:

Yes

Current State:

Final no updates expected

Accession numbers for Labyrinthulomycetes detected in sea fans collected in the Florida Keys and Puerto Rico from 2006-2010 (Climate_CoralDisease project)

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Description

Accession numbers to NCBI's GenBank are provided for Labyrinthulomycetes detected in sea fans collected in Florida and Puerto Rico.

References:
Burge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts S, Friedman CS & CD Harvell. In press (May 2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina. Dis Aquat Org.

Methods & Sampling

Sampling and Analytical Methodology:
Healthy and diseased sea fans were collected from Florida and Puerto Rico. Labyrinthulomycetes cells were isolated from a diseased sea fan from Florida; DNA extracted, amplified, cloned, sequenced, and deposited with accession # JQ248602. Fragments of healthy and diseased sea fans were extracted, amplified, cloned and sequenced under accession numbers JQ248603 (Florida), JQ248604 (Florida), JQ248605 (Puerto Rico), and JQ248606 (Puerto Rico).

Labyrinthulomycota small-subunit ribosomal DNA (SSU rRNA) specific primers, Laby-A and Laby-Y, were used (Stokes et al., 2002). Those containing bands of the expected (~ 430 bp) size were purified using the QIAquick PCR kit (Qiagen,) and sent to the Cornell University Life Sciences Core Laboratories for direct sequencing on an Applied Biosystems Automated 3730 DNA Analyzer. Although direct sequencing of all of the PCR products showed unambiguous DNA chromatographs throughout, the homogeneity of samples was additionally confirmed by cloning the PCR products into the TOPO-TA vector, using the TOPO TA cloning kit (Invitrogen) for sequencing of 2 to 5 clones of each isolate.

Data Processing Description

The BLAST algorithm (Altschul et al.1990) was used to compare resulting sequences (overlapping 398 nt from Florida samples and 292 nt from Puerto Rico samples) with those deposited in the National Center for Biotechnology Information (NCBI) GenBank database, and alignments were made using the EMBL-EBI Clustal W tool (Larkin et al. 2007, Goujan et al. 2010). Representative sequences from the cultured microorganism and sea fan isolates were submitted to GenBank.

Data Files

File
sea_fan_parasite_seq.csv (Comma Separated Values (.csv), 844 bytes) MD5:0efb013350beecb6ace3838174d929aa Primary data file for dataset ID 3718

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0849776

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Coral_Dive_HM		2006-09-01	shoreside PR_Keys_Reef	Drew Harvell (Principal Investigator) Laura Mydlarz (Co-Principal Investigator) Dr Colleen Burge (Contact)	data info

Instruments

Automated DNA Sequencer

Supplied Description:

Direct sequencing was performed at the Cornell University Life Sciences Core Laboratories on an Applied Biosystems Automated 3730 DNA Analyzer

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
site	Name of the reef where the sample was collected.	text	site
lat	Latitude of the collection site. North = positive.	decimal degrees	lat
lon	Longitude of the collection site. West = negative.	decimal degrees	lon
sequence_name	Name of the sequence/sample.	text	no_bcodmo_term
accession_number	Assigned accession number and link to GenBank.	unitless	accession_number

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Database

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Dataset: sea_fan_parasite_sequences