• Arctic SDI catalogue
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Development of a coastal species characterization approach using environmental DNA (eDNA) using the marker COI

Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of invertebrates species whose DNA has been detected in water samples collected at 2018 using the marker COI.

The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 9-52 meters depth in 40 stations with one sample par station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissue extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. Libraries at the COI locus were prepared by Genome Quebec and sequenced on an Illumina MiSeq PE250 system. The bioinformatics analysis of the sequences obtained was carried out using an in-house analysis pipeline as reported in Bourret et al. 2022. A first step made it possible to obtain a molecular operational taxonomic unit table (MOTU) using the cutadapt software for the removal of the adapters and the DADA2 R package for the filtration, fusion, chimera removal and data compilation. The MOTUs table was subsequently corrected by taking into account the negative controls, where the number of observations in the latter was removed from the linked samples. Singleton MOTUs have also been removed. Finally, the taxonomic assignments were carried out on the MOTUs using the IDTAXA classifier (present in the DECIPHIER R package) using a training set trained on the COI reference bank for Golf St-Laurent (GSL-rl v1.0, https://github.com/GenomicsMLI-DFO/MLI_GSL-rl ) and a threshold of 40. Detections with an “Unreliable due to gaps” category were reported at the genus level only.

The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute.

This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems.

Data are also available on SLGO platform : https://doi.org/10.26071/ogsl-cd4c205b-f63b

Simple

Date ( RI_367 )
2022-12-02
Date ( RI_366 )
2022-12-02
RI_418
  Government of Canada;Fisheries and Oceans Canada;Scientific Advice, Information and Support Branch - Yanick Gendreau ( Aquatic Science Biologist )
850 route de la Mer , Mont-Joli , Quebec , G5H 3Z4 , Canada
418-775-0627
RI_418
  Government of Canada;Fisheries and Oceans Canada;Scientific Advice, Information and Support Branch - Sandra Velasquez ( Aquatic Science Biologist )
850 route de la Mer , Mont-Joli , Quebec , G5H 3Z4 , Canada
418-775-0036
Status
onGoing; enContinue RI_596
Maintenance and update frequency
asNeeded; auBesoin RI_540
Keywords ( RI_524 )
  • Metabarcoding
  • COI
Keywords ( RI_525 )
  • St. Lawrence River
  • Quebec
Keywords ( RI_528 )
  • Invertebrate
Government of Canada Core Subject Thesaurus Thésaurus des sujets de base du gouvernement du Canada ( RI_528 )
  • Fish
Classification
unclassified; nonClassifié RI_484
Use limitation
Open Government Licence - Canada (http://open.canada.ca/en/open-government-licence-canada)
Access constraints
license; licence RI_606
Use constraints
license; licence RI_606
Spatial representation type
textTable; texteTable RI_637
Metadata language
eng; CAN
Metadata language
fre; CAN
Topic category
  • Oceans
  • Environment
Begin date
2018-08-11
End date
2018-08-14
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Reference system identifier
http://www.epsg.io / EPSG:4326
Distribution format
  • CSV ( 1.0 )

RI_414
  Government of Canada;Fisheries and Oceans Canada;Scientific Advice, Information and Support Branch - Gestion de données ( Biologist )
850 route de la Mer , Mont-Joli , Quebec , G5H 3Z4 , Canada
OnLine resource
Development Coastal Species Characterization eDNA COI ( ESRI REST: Map Server )

Web Service;ESRI REST;eng

OnLine resource
Data of coastal species characterization approach ( HTTPS )

Dataset;CSV;eng,fra

OnLine resource
Data dictionnary ( HTTPS )

Supporting Document;PDF;eng,fra

OnLine resource
Development Coastal Species Characterization eDNA COI ( ESRI REST: Map Server )

Web Service;ESRI REST;fra

File identifier
6319d10d-2ea7-44af-bfde-20e2da053d5a XML
Metadata language
fra; CAN
Character set
utf8; utf8 RI_458
Parent identifier
Coastal Environmental Baseline Program 7f4b9eb6-805f-4d0b-a597-2d7a44e045d7
Hierarchy level
dataset; jeuDonnées RI_622
Date stamp
2025-02-06T00:23:28.256Z
Metadata standard name
North American Profile of ISO 19115:2003 - Geographic information - Metadata
Metadata standard version
CAN/CGSB-171.100-2009
RI_419
  Government of Canada;Fisheries and Oceans Canada;Demersal and Benthic Science Branch - Audrey Bourret ( Aquatic Sciences Biologist )
850 route de la Mer , Mont-Joli , Quebec , G5H 3Z4 , Canada
418-775-0647
RI_418
  Government of Canada;Fisheries and Oceans Canada;Science Advice, Information and Support Branch - Sandra Velasquez ( Aquatic Sciences Biologist )
Canada , Mont-Joli , Quebec , G5H 3Z4 , Canada
418-775-0036
 
 

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Map of stations
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