Dataset: Acropora palmata genotypes for clonal age
Deployment: Baums_Carib

Mutations at microsatellite loci of Acropora palmata

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/666350

Principal Investigator:

Iliana B. Baums (Pennsylvania State University, PSU)

BCO-DMO Data Manager:

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

Project:

Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction? (Coral Hybridization)

Current State:

Preliminary and in progress

Version:

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Description

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. Two multiplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay five loci containing AAT repeats. These five microsatellite loci have previously been demonstrated to be mendelian and coral-specific using controlled crosses (Baums et al., 2005). 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 3.0 (Applied Biosystems, CA). Alleles were scored as PCR product size.

References:

Baums IB, Devlin-Durante MK, LaJeunesse TC (2014) New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Molecular Ecology 23, 4203-4215.

Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Marine Ecology - Progress Series 288, 115-127 for details on PCR amplification.

Devlin-Durante MK, Miller MW, Caribbean Acropora Research G, Precht WF, Baums IB. How old are you? Genet age estimates in a clonal animal. Mol Ecol. 2016. doi: 10.1111/mec.13865 for details on how mutations were scored.

Data Processing Description

Dataset Processing Description

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

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- nd (no data) was entered into all blank cells
- replaced spaces and / with underscores
- converted the submitted multilevel table to a flat table

VERSIONS: 2017-21-26: Replaced version 1 (2016-11-30) with version 2 (2017-10-19). There was a shift in 1 basepair at locus 181 for some of the data.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1537959	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: automated sequencer (ABI 3730)

Supplied Description:

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.

Thermal Cycler

Supplied Name: ABI 3730

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
region	sampling region	unitless	region
database_id	Baums lab sample Database ID (unique for each sample)	unitless	sample
genet_id	Genets are identified by their Genet ID. All samples that share all ancestral alleles at five microsatellite loci were assigned the same genet ID. See methods for how ancestral alleles were determined.	unitless	sample
mutant_id	A Unique ID given to each unique multilocus genotype. This multilocus genotype includes all alleles (diploid ancestral and additional mutations).	unitless	sample
locus	the microsatellite locus that had a mutated allele (166; 181; 182; 192; 207)	basepairs	no_bcodmo_term
size_bp	size of allele?	basepairs	no_bcodmo_term
allele	allele identifier	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: Acropora palmata genotypes for clonal ageDeployment: Baums_Carib

Dataset acquisition description

Dataset Processing Description

Dataset: Acropora palmata genotypes for clonal age
Deployment: Baums_Carib