Dataset: Acropora palmata mutations
Deployment: Baums_Carib

Mutations at microsatellite loci of Acropora palmata

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)

Version Date:

2017-10-19

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/666349/data

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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.

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
- sorted records by region

VERSIONS: 2017-10-26: Replaced version 1 (2016-11-30) with version 2 (2017-10-19). Some latitudes and longitudes were added to allow visualization of the data on the mapserver.

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
reef	the sampling reef	unitless	site
database_id	Baums lab sample Database ID (unique for each sample)	unitless	sample
locus	the microsatellite locus that had a mutated allele (166; 181; 182; 192;207)	basepairs	no_bcodmo_term
ancestral_allele_1	the first ancestral alleles of the genet	basepairs	no_bcodmo_term
ancestral_allele_2	the second ancestral alleles of the gene	basepairs	no_bcodmo_term
allele_3	any additional alleles detected	basepairs	no_bcodmo_term
allele_4	any additional alleles detected	basepairs	no_bcodmo_term
origin_allele_3	designation of origin of how additional allele 3 arose (i.e from ancestral Allele 1 or Allele 2). Sometimes one ancestral allele mutated twice giving rise to Alleles 3 and 4.	basepairs	no_bcodmo_term
origin_allele_4	designation of origin of how additional allele 4 arose (i.e from ancestral Allele 1 or Allele 2). Sometimes one ancestral allele mutated twice giving rise to Alleles 3 and 4.	basepairs	no_bcodmo_term
mutation_step_allele_3	Count of mutation steps from ancestral allele to mutated allele. Each mutation step is an addition or loss of 3 bp.	basepairs	no_bcodmo_term
mutation_step_allele_4	Count of mutation steps from ancestral allele to mutated allele. Each mutation step is an addition or loss of 3 bp.	basepairs	no_bcodmo_term
mutational_change_allele_3_bp	Mutational Change Allele 3 (bp) The mutational change (in bp) from the ancestral alleles to the new allele is given.	basepairs	no_bcodmo_term
mutational_change_allele_4_bp	Mutational Change Allele 4 (bp) The mutational change (in bp) from the ancestral alleles to the new allele is given.	basepairs	no_bcodmo_term
sample_count_for_genet	Genets had from 2 to 94 samples (sample count for genet)	samples	no_bcodmo_term
genet_id	Genets are identified by their Genet ID	unitless	no_bcodmo_term
full_mutation	Sometimes ancestral alleles were no longer detected (full mutations)	unitless	no_bcodmo_term
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon

Database

Contribute Data

Dataset: Acropora palmata mutationsDeployment: Baums_Carib

Dataset acquisition description

Dataset Processing Description

Dataset: Acropora palmata mutations
Deployment: Baums_Carib