Dataset: Metadata for targeted genotyping of green crabs in the northeast Pacific

Name: Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022
Published: 2025-01-27
Keywords: Carcinus maenas, population genetics, marine invasion, biota, inlandWaters, oceans

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Spatial Extent: N:49.606306 E:-122.422437 S:43.347281 W:-124.323273

Coastal northeastern Pacific in the range of Carcinus maenas, from California to British Columbia.

Temporal Extent: 2016-08-17 - 2022-10-12

Project:

Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator (West Coast Carcinus)

Principal Investigator:

Carolyn Tepolt (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Emily Grason (Sea Grant, WSG)

Patrick McDonald (University of Washington, UW)

Scientist:

Adrianne Akmajian (Makah Tribe)

Shon Schooler (South Slough National Estuarine Research Reserve)

Sylvia Behrens Yamada (Oregon State University, OSU)

BCO-DMO Data Manager:

Audrey Mickle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2025-01-27

Restricted:

Validated:

Current State:

Preliminary and in progress

Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022

Abstract:

This project explores genetic changes in the invasive European green crab (Carcinus maenas) in the northeast Pacific, using targeted genotyping of SNPs identified in prior high-resolution population genomics in the region. It tracks the early stages of green crab invasion into a new environment, particularly through repeated sampling of multiple size-classes of crabs from the same sites over multiple years. Samples span time and space across the species range in the northeast Pacific, with a focus on the coast of Washington and Oregon. This dataset includes individual collection and accession metadata for 1,662 crabs, for which raw demultiplexed reads are archived at GenBank's SRA under BioProject PRJNA1177418.

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Methods & Sampling

Samples of Carcinus maenas (urn:lsid:marinespecies.org:taxname:107381) were collected by large network of collaborators, usually by trapping but approaches vary. Crabs were first frozen at -20C, then muscle or gill tissue was dissected out, preserved in 95% ethanol, and archived at -80C. Genomic DNA was extracted with Chelex 100 resin. Targeted genotyping of ~200 SNPs was conducted following the approach of Campbell et al. 2015; target SNPs were identified in prior population genomics analysis in the region based on RNA-Seq data. Samples were prepared in two groups, with overlapping but not identical targets; some samples were normalized using SequalPrep plates and others were not, following results of replicate sequencing with ("norm" in sequence names) and without normalization showing that this step did not improve genotyping success. Libraries were individually dual-indexed with plate and well barcodes, and multiplexed 800-1500 / lane on two lanes of 150 bp paired-end Illumina NovaSeq X 10B sequencing at the University of California at Berkeley's QB3 Genomics Core lab. Some samples were re-run across multiple plates / lanes as technical replicates ("repA" and "repB" in sequence names).

Problems/Issues

Some dates, latitude, longitude, and collector information was not reported. Those values are represented as blanks. Sampling coordinates are withheld for samples collected in Makah tribal waters. To request coordinates for these samples, please contact Adrianne Akmajian (marine.ecologist@makah.com).

Data Processing Description

Samples were demultiplexed by UC Berkeley's QB3 Genomics Core lab, and are provided raw with no further processing.

BCO-DMO Processing

- Imported "BCO-DMO_GTSeq_metadata_NSF-1850996.csv" into BCO-DMO system
- Replaced "â€™" with "'" in collector_affiliation field
- Replaced "10-2018-11" with "2018-11" in collection_date field
- Exported file as "949610_v1_green_crab_collection"

Accepted species identifier confirmed on 2025-01-29.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1850945
NSF Division of Ocean Sciences	OCE-1850996

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina NovaSeq X 10B

Supplied Description:

Illumina NovaSeq X 10B sequencing (150 bp paired-end), conducted at University of California at Berkeley's QB3 Genomics Core lab

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_name	Individual sample ID	unitless	sample
SRA_accession	SRA accession number for individual sequence files	unitless	SRA_run
biosample_accession	Individual NCBI BioSample code	unitless	BioSample
embayment	General coastal water body from which sample was collected	unitless	site
site	More specific data on collection location provided by collector	unitless	site
state	US state or Canadian province where samples was collected	unitless	region
sex	Sex (M=Male, F=Female, or U=Unknown)	unitless	sex
size_CW	Carapace width of crab in mm	Millimeters (mm)	width
color	Color of ventral side of cephalothorax, as determined by collector	unitless	sample_descrip
collection_date	Date of collection to the level of specificity available	unitless	date
latitude	Latitude of collection; positive values = North	decimal degrees	lat
longitude	Longitude of collection; positive values = East	decimal degrees	lon
collector	Person who collected the sample	unitless	person
collector_affiliation	Organization through which the sample was collected	unitless	sample_descrip

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Dataset: Metadata for targeted genotyping of green crabs in the northeast Pacific