Dataset: Haloptilus longicornis SRA

Name: Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project)
Published: 2017-05-15
Keywords: Genome concordance, Haloptilus longicornis, holoplankton, RADseq, sympatric speciation, zooplankton, biota, oceans

View Data: Data not available yet

Cite This Dataset

Project:

Basin-scale genetics of marine zooplankton (Plankton Population Genetics)

Principal Investigator:

Erica Goetze (University of Hawaiʻi at Mānoa, SOEST)

BCO-DMO Data Manager:

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

Version:

Version Date:

2017-05-15

Restricted:

Yes

Release Date:

2021-01-01

Validated:

Current State:

Preliminary and in progress

Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project)

Abstract:

Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata

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Description

This data submission consists of specimen collection information and next-generation sequencing data (Illumina MiSeq v3 - 300bp PE reads) from pooled DNA libraries of three putative Haloptilus longicornis clades that have sympatric distributions in the North Atlantic Ocean. Specimens were collected during the 2010 Atlantic Meridional Transect cruise (AMT20). 113 total H. longicornis were pooled into three clades as defined by reciprocal monophly and fixed differences in mtDNA cytochrome oxidase c subunit II. The aim of this project is to utilize reduced representation genomic data to assess whether there is concordance between the three putative H. longicornis clades demarcated with mtCOII and clades determined using other regions of the genome. Earlier work indicates only two clades are detected using microsatellite loci, and this project will broaden the genomic scope of that investigation.

The sequences are archived at NCBI, BioProject PRJNA369182 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA369182]

The publisher requires that this item is embargoed until 2018-01-01. Please check back after 2018-01-01.

Methods & Sampling

If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.

From the cruise report: not yet available

Sample collection. A total of 113 H. longicornis individuals from three putative clades were collected from five different locations in the North Atlantic Basin during the Atlantic Meridional Transect cruise in 2010 (AMT20) for this analysis. 81 individuals from putative clade 1 were collected from two sites, 20 individuals from putative clade 2 were collected from four sites (one of which was the same as one of the clade one locations), and 12 individuals from putative clade 3 were collected from the same four sites as the clade 2 individuals.

Data Processing Description

Contact: Erica Goetze for any questions, or for subsequent use of these data.

BCO-DMO Processing Notes:
added conventional header with dataset name, PI name, version date
modified parameter names to conform with BCO-DMO naming conventions
combined SRA metadata with collection information
converted latitude and longitude to decimal degrees

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1338959

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
JC079	AMT22 Atlantic Meridional Transect Cruise 22	2012-10-10	RRS James Cook	Glen Tarran (Chief Scientist)	data info
JC053	AMT20 Atlantic Meridional Transect Cruise 20	2010-10-12	RRS James Cook	James Rees (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2500

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.

Bongo Net

Supplied Name: WP2

Supplied Description:

200µm mesh size; 0-300 meters vertical haul to collect copepods.

Instrument Type

Generic Name: Bongo Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0009/

Generic Description:

A Bongo Net consists of paired plankton nets, typically with a 60 cm diameter mouth opening and varying mesh sizes, 10 to 1000 micron. The Bongo Frame was designed by the National Marine Fisheries Service for use in the MARMAP program. It consists of two cylindrical collars connected with a yoke so that replicate samples are collected at the same time. Variations in models are designed for either vertical hauls (OI-2500 = NMFS Pairovet-Style, MARMAP Bongo, CalVET) or both oblique and vertical hauls (Aquatic Research). The OI-1200 has an opening and closing mechanism that allows discrete "known-depth" sampling. This model is large enough to filter water at the rate of 47.5 m3/minute when towing at a speed of two knots. More information: Ocean Instruments, Aquatic Research, Sea-Gear

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
bioproject_accession	NCBI BioProject accession number	unitless	sample
biosample_accession	NCBI BioSample accession number	unitless	sample
cruise_id	cruise identifier	unitless	cruise_id
date_collection	collection date formatted as yyyy-mm-dd	unitless	date
design_description	NCBI Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.	unitless	no_bcodmo_term
filename	NCBI file name	unitless	file_name
lat_collection	latitude; north is positive	decimal degrees	lat
library_ID	NCBI Library identifier	unitless	no_bcodmo_term
lon_collection	longitude; east is positive	decimal degrees	lon
sample_name	short sample identifier	unitless	sample
station	station number	unitless	sta
title	NCBI sample title	unitless	sample

Status message

Database

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Dataset: Haloptilus longicornis SRA