Dataset: dataset2_Krug_et_al_2012: Elysia accessions
Deployment: Krug_lab

Elysia spp. accessions for COI, 16S, H3

Principal Investigator:

Patrick Krug (California State University Los Angeles, Cal State LA)

BCO-DMO Data Manager:

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

Project:

Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions (PLDvFST)

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/679926/data

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Description

Specimens of two species of Elysia (Gastropoda: Sacoglossa) were sequenced from the Caribbean (E. cornigera) and the Mediterranean (E. timida).

Related Reference: Krug, P.J., Händeler, K., and J.E. Vendetti. 2012. Genes, morphology, development and photosynthetic ability support the resurrection of Elysia cornigera (Heterobranchia: Plakobranchoidea) as distinct from the solar-powered sea slug E. timida. Invertebrate Systematics, 25: 477–489. (doi: 10.1071/IS11026)

Methods & Sampling

Dataset acquisition description

Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems). Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.

For full details on sampling and analytical methodology, see Krug et al (2012).

Data Processing Description

Dataset Processing Description

Sequences were edited to remove primer sequences.

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
- converted latitude and longitude to decimal degrees
- added column with species name and removed columns with species specimen count totals
- added links to NCBI accessions

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1130072	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).

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:

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
species	species name	unitless	species
collection_locality	collection location	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
date_collected	collection date formatted as m-yyyy	unitless	date
NCBI_COI_accession	COI gene GenBank accession number	unitless	accession_number
NCBI_16S_accession	16S gene GenBank accession number	unitless	accession_number
NCBI_H3_accession	H3 gene GenBank accession number	unitless	accession_number
NCBI_COI_accession_link	link to COI gene GenBank accession page	unitless	external_link
NCBI_16S_accession_link	link to 16S gene GenBank accession page	unitless	external_link
NCBI_H3_accession_link	link to H3 gene GenBank accession page	unitless	external_link

Database

Contribute Data

Dataset: dataset2_Krug_et_al_2012: Elysia accessions
Deployment: Krug_lab

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: dataset2_Krug_et_al_2012: Elysia accessionsDeployment: Krug_lab

Dataset acquisition description

Dataset Processing Description

Dataset: dataset2_Krug_et_al_2012: Elysia accessions
Deployment: Krug_lab