Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020

Abstract

These files support the publication "Multiple lineages of transmissible neoplasia in the basket cockle (C. nuttallii) with repeated horizontal transfer of mitochondrial DNA," which has been submitted to bioRxiv (doi:10.1101/2023.10.11.561945). Details of locations and dates of cockle collection, specific primer sequences, methods for design of the primers, and analysis of results can be found there.

These files are fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State. For each cockle DNA was extrcted from a solid tissue sample (T) and a hemolymph sample (H). These were used to identify bivalve transmissible neoplasia in several cockle samples in these populaitons (together with other genetic data from other nuclear and mitochondrial markers). Microsatellites were amplified from DNA extracted from both hemocyte and tissue using Taq polymerase (Genesee Scientific) for a select number of individuals: all possible neoplastic animals based on positive qPCR screen (n=26) and one randomly selected, non-neoplastic animal from each collection (n=12). Microsatellites were amplified using primers for 8 polymorphic loci: Cnu48, Cnu55, Cnu58, Cnu63, Cnu68, Cnu72, Cnu78, and Cnu81. Allele sizes were identified by fragment analysis using fluorescent primers (6-FAM, PET, NED, and VIC) and a 3730xl Genetic Analyzer with the LIZ-500 size standard (Applied Biosystems, operated by Genewiz). For each sample, two reactions were run: "1" with (Cnu48, blue; Cnu55, yellow; Cnu58, red; Cnu63, green) and "2" with (Cnu68, blue; Cnu72, yellow; Cnu79, red; Cnu81, green).

For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/940678