©2020 Biological and Chemical Oceanography Data Management Office.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 foc...
Show moreSamples 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).
Tepolt, C., Grason, E., McDonald, P., Akmajian, A., Yamada, S. B., Schooler, S. (2025) Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-01-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949610.1 [access date]
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