Rodriguez et al., 2024 eDNA Extraction Ring Test Sanger Sequence Data

This dataset is supplemental to the manuscript titled "Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays". The file contains Sanger sequencing results in FASTA format from environmental DNA (eDNA) samples that were collected, amplified, and sequenced as part of a study aimed at detecting marine megafauna species using qPCR. The samples were processed at multiple institutions, following various protocols described below.<b>Methodology Overview</b>qPCR Amplification and Purification: At multiple institutions (University of Innsbruck - UIBK, National Research Institute for Agriculture, Food, and the Environment - INRAE, University College Cork - UCC, and Institute of Marine Research - IMR), target species DNA from eDNA samples was amplified using qPCR, with positive amplifications subsequently purified using a variety of protocols: UIBK and IMR used ExoSAP-IT® for enzymatic cleanup (Affymetrix-USB Corporation). UCC used the QIAquick Gel Extraction Kit (Qiagen). INRAE re-amplified positive qPCR amplifications via conventional PCR then used the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel).Sanger Sequencing: Following purification, purified (q)PCR products were sequenced using Sanger sequencing. For samples from UIBK and UCC, sequencing was conducted by Eurofins Genomics (Germany). For samples from INRAE, GenoScreen (France) performed the sequencing. IMR utilized the BigDye™ Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems™) on their samples then sent products to the University of North Norway (Norway) performed sequencing.Sequence Processing: Low quality regions were identified and removed from the raw sequences using Bioedit 7.7, AliView 1.28, Geneious 7.1.9, and UGENE 50.0. Final sequence data were subjected to BLAST analysis (NCBI) for taxonomic classification, verifying matches to the target species.<b>Data Details</b>File Type: FASTA (.fas)Contents: Verified DNA sequences of target species from Sanger sequencing, following purification and amplification via qPCR.Software Used: Bioedit, AliView, Geneious, UGENE for sequence trimming; BLAST (NCBI) for taxonomic identification.<b>Purpose of the Data</b>These sequences confirm the presence of each target species in the environmental DNA samples - verified through qPCR and validated by Sanger sequencing. The dataset provides a key resource for further taxonomic and ecological studies involving species detection in marine environments using eDNA methods.