Dataset: Acropora palmata symbiont genotypes
Deployment: Baums_FL_Keys_NMS

Symbiodinium ‘fitti’ multilocus genotypes derived from 13 microsatellite markers

Principal Investigator:

Iliana B. Baums (Pennsylvania State University, PSU)

Co-Principal Investigator:

Dana E. Williams (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

Contact:

Meghann Durante (Pennsylvania State University, PSU)

Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

RAPID: surviving climate change - the role of acclimatization in reef-building corals (Surviving Climate Change)

Current State:

Preliminary and in progress

Version:

2016-01-29

Version Date:

2016-01-29

Data URL:

https://www.bco-dmo.org/dataset-deployment/637487/data

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Description

Symbiodinium ‘fitti’ (ITS2 clade A3) symbiont genotypes from Acropora palmata

Methods & Sampling

Dataset acquisition description

Adult Acropora palmata colonies were sampled (1 cm²) with hammer and chisel and tissues were preserved in 96% non-denature Ethanol. DNA was extracted using the DNEasy tissue kit (Qiagen) following manufacturer’s instructions. Thirteen singleplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay 13 loci containing tri repeats and one di repeat. PCR products were visualized with an automated sequencer (ABI 3730). An internal size standard (Gene Scan 500-Liz, Applied Biosystems CA) ensured accurate sizing. Electropherograms were analyzed with GeneMapper Software 5.0 (Applied Biosystems, CA). Alleles were scored as PCR product size in basepairs.

For quality detailed protocol and quality control please see Pinzon et al 2010 and Baums et al. 2014.

Data Processing Description

Dataset Processing Description

Electropherograms of microsatellite alleles were scored for allele sizes (basepairs) in Genemapper vers. 5.0 (Applied Biosystems) and transferred to a Filemaker Database.

BCO-DMO Processing Notes:

- Added PI-provided lat/lon for each "Reef" location.

- Edited primer column where two alleles were present in one column to split into separate columns (i.e., allele size 1 was the first 3 digits, and allele size 2 were the second consecutive digits of a six digit column. These were separated into
separate columns per allele size at each locus).

- Edited entire header to BCO-DMO format (e.g., lowercase names, underscores where needed)

- Edited lat/lon values to four decimal precision consistently.

- Edited spaces in reef names to underscores.

- Edited zero value allele sizes to 'nd' as per PI.

- Split date into year, month, day fromat.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1516763	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: automated sequencer

Supplied Description:

Applied Biosystems 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

Supplied Name	Supplied description	Supplied Units	Standard Name
region	Region where coral colony was sampled.	dimensionless	region
reef	Reef where coral colony was sampled.	dimensionless	site
lat	Latitude component of geographic sampling location; where positive is North.	decimal degrees	lat
lon	Longitude component of geographic sampling location; where positive is East.	decimal degrees	lon
colony	Colony identification number	dimensionless	sample
sample	Sample identification number consisting of colony identification number and replicate character (A-Z)	dimensionless	sample
ID_database	Baums Database access number	dimensionless	individual
primer_1	Allele size 1 for locus 1.	base pairs	no_bcodmo_term
primer_3	Allele size 1 for locus 3.	base pairs	no_bcodmo_term
primer_7	Allele size 1 for locus 7.	base pairs	no_bcodmo_term
primer_9	Allele size 1 for locus 9.	base pairs	no_bcodmo_term
primer_18	Allele size 1 for locus 18.	base pairs	no_bcodmo_term
primer_27	Allele size 1 for locus 27.	base pairs	no_bcodmo_term
primer_28	Allele size 1 for locus 28.	base pairs	no_bcodmo_term
primer_31	Allele size 1 for locus 31.	base pairs	no_bcodmo_term
primer_32	Allele size 1 for locus 32.	base pairs	no_bcodmo_term
primer_41	Allele size 1 for locus 41.	base pairs	no_bcodmo_term
primer_41_allele2	Allele size 2 for locus 41.	base pairs	no_bcodmo_term
primer_2	Allele size 1 for locus 2.	base pairs	no_bcodmo_term
primer_2_allele2	Allele size 2 for locus 2.	base pairs	no_bcodmo_term
primer_8	Allele size 1 for locus 8.	base pairs	no_bcodmo_term
primer_48	Allele size 1 for locus 48.	base pairs	no_bcodmo_term
primer_48_allele2	Allele size 2 for locus 48.	base pairs	no_bcodmo_term
year	year of sample collection.	YYYY	year
day_local	day of sample collection.	DD	day_local
month_local	month of sample collection.	MM	month_local

Database

Contribute Data

Dataset: Acropora palmata symbiont genotypesDeployment: Baums_FL_Keys_NMS

Dataset acquisition description

Dataset Processing Description

Dataset: Acropora palmata symbiont genotypes
Deployment: Baums_FL_Keys_NMS