Dataset: P. xiphias SRA

Name: Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project)
Published: 2017-03-08
Keywords: biota, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:39.647 E:-22.4662 S:-39.88 W:-42.0517

Temporal Extent: 2012-10-16 - 2012-11-17

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:

2017-03-08

Restricted:

Yes

Release Date:

2021-01-01

Validated:

Current State:

Preliminary and in progress

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

Abstract:

Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata

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Description

This dataset includes RADSeq data as well as NCBI Short Read Archive (SRA) BioProject and BioSample accessions and collection metadata from animals collected on Atlantic Meridional Transect 22 (AMT22) in Oct. - Nov. 2012. Field work was conducted on the RRS James Cook cruise JC079. See NCBI GenBank Bioproject PRJNA368728 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA368728]

The sequences are embargoed until 2019-12-01. Please check back after that date.

README for processed data files associated with the article: “Genetic isolation between populations in distinct pelagic habitats of the oceanic copepod Pleuromamma xiphias” – Authors: Lauren Van Woudenberg, Matthew Iacchei, Jonathon Whitney, Katja T. C. A. Peijnenburg, Erica Goetze (2017?). in preparation for submission to Molecular Ecology.

Data files included in this archive:
(1) Supplementary Table 1. Overview of RADSeq data for all animals included in the study. VanWoudenberg_et_al_PLXI_RADSeq.xlsx

(2) VCF file used in downstream analyses, including mitochondrial clade 3 animals only. 289 total animals included. M4n3_5X_60%indiv_40%miss_final.vcf.

(3) VCF file used in downstream analyses, for analyses regarding mitochondrial clades 2 & 3 and SNP clusters 1 & 2. 112 total animals included. MTclades_M4n3_5X_60%indiv_40%miss.vcf

(4) Summary table and metadata of the sequence files submitted to the NCBI Sequence Read Archive (SRA), with BioProject and BioSample numbers. VanWoudenberg_et_al_2017_SRA_metadata.xlsx

Methods & Sampling

Please refer to the paper for methodological details. If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.

From the cruise report:
Sample collection. Plankton samples were collected with 0.71m diameter bongo nets (200, 333 µm), and with an RMT1 midwater trawl (333 µm) that has a nominal mouth area of 1m2. A total of 50 plankton tows were conducted along the cruise leg (Table 1), with 35 tows conducted using the bongo and 14 samples collected with the RMT net. The bongo tows were oblique tows that sampled from between 211 to 488 m depth and the surface (324m average maximum depth of tow). The bongo samples will be used for quantitative estimates of animal abundance along the cruise leg (target species only, tows conducted with timedepth-recorder and flowmeter). The RMT tows were also oblique tows that sampled between 62 to 216 m depth and the surface (153 m average maximum depth of tow). All tows except one (station 42) were conducted at night, in order to efficiently sample the migratory community.

Sample handling and preservation. All plankton from the 200 µm mesh bongo net was preserved immediately in 100% ethyl alcohol for use in molecular studies, including DNA sequencing and microsatellite genotyping (and possibly RAD tag sequencing), in addition to estimates of abundance of target species. Plankton material from the 333 µm mesh bongo net and the RMT net was sorted live immediately following collection, and animals were individually identified, and preserved in acetone, RNALater, cryopreserved, and in some cases used for live imaging prior to preservation. These animals will be used for molecular, genomic and transcriptomic analyses. Both RNA/DNA ratios and prosome length - dry weight relationships will be used as measures of animal condition in copepods. In total, over 17,000 animals from 40 target species were individually sorted and preserved for this panel of measurements. Following live sorting and imaging of the 333 µm samples, the remaining plankton was preserved either in 4% buffered formalin or 100% ethyl alcohol for morphological studies.

Data Processing Description

SEQUENCE DATA FILES
Illumina HiSeq reads are available NCBI Sequence Read Archive (SRA). Libraries were prepared following the ezRAD protocol (Toonen et al. 2013). Sequences from Illumina HiSeq 2500, with quality trimming and adaptor removal using TrimGalore (as follows).

#ADAPTERS
#Illumina TruSeq HT dual-indexed Adapters (96 barcode combinations)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG #Read1 w/ 8 digit wildcard i7 #barcode
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT #Read2 w/ wildcard i5 barcode (reverse complemented)

#TrimGalore Command
#first make directory for cleaned files
mkdir cleaned_for_stacks

##FOR R1 loop for trim_galore##
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)

for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcacacgtctgaactccagtcacnnnnnnnnatctcgtatgccgtcttctgcttg --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R1.fq; done

##FOR R2 loop for trim_galore##
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)

for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcgtcgtgtagggaaagagtgtnnnnnnnngtgtagatctcggtggtcgccgtatcatt --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R2.fq; done

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
added links to NCBI GenBank BioProject and BioSample pages

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

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.

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
library_ID	NCBI Library identifier	unitless	no_bcodmo_term
title	NCBI project title	unitless	no_bcodmo_term
library_strategy	NCBI term meaning genomic method used for analysis	unitless	no_bcodmo_term
library_source	NCBI term meaning the type of genomic material that was analyzed	unitless	no_bcodmo_term
library_selection	NCBI term meaning method that the source material was selected	unitless	no_bcodmo_term
library_layout	NCBI library layout: Paired-end or Single	unitless	no_bcodmo_term
platform	platform used for sequencing	unitless	platform
instrument_model	sequencing instrument model	unitless	instrument
design_description	NCBI	unitless	no_bcodmo_term
filetype	type of file	unitless	no_bcodmo_term
filename	file name	unitless	file_name
sample_id	sample identifier	unitless	sample
cruise_id	cruise identifier	unitless	cruise_id
sta	station number	unitless	sta
lat_collection	latitude; north is positive	decimal degrees	lat
lon_collection	longitude; east is positive	decimal degrees	lon
date_collection	collection date formatted as yyyy-mm-dd	unitless	date
sex	sex of specimens	unitless	sex
mtCOI_Clade	mitochondrial COI clade	unitless	taxon
num_Seq_reads_initial	number of sequence reads pre-cleaning	reads	no_bcodmo_term
num_Seq_reads_post_cleaning	number of sequence reads post-cleaning	reads	no_bcodmo_term

Status message

Database

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Dataset: P. xiphias SRA