Dataset: dataset5_Vendetti_et_al_2012: Elysia pusilla sequences

Name: GenBank accessions and links for sequences of three genes (COI, 16S, H3) for five Elysia spp., chiefly E. pusilla: Vendetti et al (2012) Integ. and Comp. Biol. (PLDvFST project)
Published: 2017-01-26
Keywords: biota, oceans

Cite This Dataset

Project:

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

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)

Version Date:

2017-01-26

Restricted:

Validated:

Yes

Current State:

Final no updates expected

GenBank accessions and links for sequences of three genes (COI, 16S, H3) for five Elysia spp., chiefly E. pusilla: Vendetti et al (2012) Integ. and Comp. Biol. (PLDvFST project)

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Description

Sequences for three genes (COI, 16S, H3) were generated for five Elysia species sampled across the Pacific (E. pusilla, E. stylifera) and Caribbean (other species). Collection information, accessions, and links to the GenBank pages are provided.

'did_not_amplify ' means that a locus that did not amplify;
'n/a' means that no amplification was attempted in the present study
'nd' means that the allelic phase was not resolved from genotypic sequence data

Related Reference: Vendetti, J.E., Trowbridge, C.D., and P.J. Krug. 2012. Poecilogony and population genetic structure in Elysia pusilla (Heterobranchia: Sacoglossa), and reproductive data for five sacoglossans that express dimorphisms in larval development. Integrative and Comparative Biology, 52: 138-150. doi: 10.1093/icb/ics077

Methods & Sampling

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 Vendetti et al (2012).

Data 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
- added links to NCBI accessions
- replaced hyphens with 'did_not_amplify'
- copied information from previous haplotype or allele to fill out table; if none matched, nd (no data) was entered into blank cells in accession columns

Data Files

File
dataset5_Vendetti_2012.csv (Comma Separated Values (.csv), 12.02 KB) MD5:0c4812c7831ffbb6ab2c37f67474e8b5 Primary data file for dataset ID 682268

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Krug_lab		2011-09-01	Cal State LA	Patrick Krug (Principal Investigator)	data info

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
specimen_code	in-house specimen identifier	unitless	sample
species	specimen identifier code	unitless	species
Histone_3_allele	Histone 3 allele identifier	unitless	no_bcodmo_term
haplotype_COI	haplotype COI identifier	unitless	no_bcodmo_term
haplotype_16S	haplotype 16S identifier	unitless	no_bcodmo_term
date_collected	date collected	unitless	date
collection_locality	place of collection	unitless	site
accession_H3_link	link to H3 gene GenBank accession page	unitless	external_link
accession_H3	H3 gene GenBank accession number	unitless	accession_number
accession_COI_link	link to COI gene GenBank accession page	unitless	external_link
accession_COI	COI gene GenBank accession number	unitless	accession_number
accession_16S_link	link to 16S gene GenBank accession page	unitless	external_link
accession_16S	16S gene GenBank accession number	unitless	accession_number

Status message

Database

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Dataset: dataset5_Vendetti_et_al_2012: Elysia pusilla sequences