{"help":"https://catalogue.cioos.ca/api/3/action/help_show?name=package_show","success":true,"result":{"id":"27a6aea7-2c94-408e-a910-592c40d10083","ecv":[],"eov":["other"],"url":null,"name":"ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea","tags":[],"type":"dataset","notes":"La caractérisation des espèces par l’ADN environnemental (ADNe) est une méthode qui permet d’utiliser l’ADN libéré dans l’environnement par les organismes de diverses sources (sécrétions, fèces, gamètes, tissus, etc.). C’est un outil complémentaire aux méthodes standards d’échantillonnage pour l’identification de la biodiversité. Ce projet fournit une liste d’espèces d’invertébrés dont l’ADN a été détecté dans des échantillons d’eau collectés en 2018 à l’aide du marqueur COI.\n\nLe relevé a été réalisé à l’été 2018 du 11 au 14 août, entre Forestville et Godbout (Haute-Côte-Nord) à partir du navire NGCC Leim. L’échantillonnage a été réalisé entre 9-52 mètres de profondeur dans 40 stations, avec un seul échantillon par station. Deux litres d’eau ont été filtrés sur un filtre en fibre de verre de 1.2 µm. Les extractions de l’ADN ont été effectuées avec le kit d’extraction *DNeasy Blood and Tissue (Qiagen)*. Des contrôles négatifs de terrains, d’extractions et de PCR ont été ajoutés aux différentes étapes du protocole. Les librairies au locus COI ont été préparées par Génome Québec et séquencées sur un système Illumina MiSeq PE250. L’analyse bio-informatique des séquences obtenues a été réalisée à l’aide d’un pipeline d’analyse maison tel que rapporté dans Bourret et al. (2022). Une première étape a permis l’obtention d’une table d’unité moléculaire opérationnelle de taxonomie (ou *Molecular operational taxonomic* unit, MOTU) à l’aide du logiciel Cutadapt pour le retrait des adaptateurs et du paquet R DADA2 pour la filtration, la fusion, le retrait des chimères et la compilation des données. La table de MOTUS a par la suite été corrigée en prenant compte des témoins négatifs, où le nombre d’observations dans ces derniers a été retiré des échantillons liés. Les MOTUs singletons ont également été retirés. Finalement, les assignations taxonomiques ont été effectuées sur les MOTUs à l’aide du classificateur IDTAXA (présent dans le paquet R DECIPHIER) en utilisant un *training set* entraîné sur la [banque de référence COI pour le golfe du Saint-Laurent](https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) et un seuil de 40. Les détections avec une catégorie « *Unreliable due to gaps* » ont été rapportées au niveau du genre uniquement. \n\nLes fichiers fournis comprennent les informations génériques de l'activité, notamment le site, le nom de la station, la date, le type de marqueur, les types des assignations utilisées pour l’identification des taxons et une liste de taxons ou espèces . La liste de taxons a été vérifiée par un expert en biodiversité de l'Institut Maurice-Lamontagne. \n\nCe projet a été financé par le Programme sur les données environnementales côtières de référence de Pêches et Océans Canada dans le cadre du Plan de protection des océans. Cette initiative vise à acquérir des données environnementales de base qui contribuent à la caractérisation des zones côtières d’importance et appuient des évaluations fondées sur des preuves ainsi que les décisions de gestion afin de préserver les écosystèmes marins. Consultez le jeu de données aussi disponible sur le portail de [**Données Ouvertes Canada**](https://ouvert.canada.ca/data/fr/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a).","state":"active","title":"Utilisation du marqueur COI pour le développement d’une approche de caractérisation des espèces côtières à l’aide d’ADN environnemental (ADNe)","author":null,"extras":[{"key":"access_constraints","value":""},{"key":"contact-email","value":"Sandra.Velasquez@dfo-mpo.gc.ca"},{"key":"encoding","value":"utf8"},{"key":"guid","value":"ca.cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea"},{"key":"h_job_id","value":"4b000124-58ec-4fba-919d-d2ad1bee305b"},{"key":"h_object_id","value":"dab823a2-670c-423a-9c95-96102b5636ce"},{"key":"h_source_id","value":"61cbaa40-5cef-4ff5-9501-2e8b641bec14"},{"key":"h_source_title","value":"St. Lawrence Global Observatory"},{"key":"h_source_url","value":"https://catalogue.ogsl.ca"},{"key":"harvest_object_id","value":"dab823a2-670c-423a-9c95-96102b5636ce"},{"key":"harvest_source_id","value":"61cbaa40-5cef-4ff5-9501-2e8b641bec14"},{"key":"harvest_source_organization","value":"{\"id\": \"b9a157db-ac56-4a28-aee9-899a35f463c6\", \"name\": \"slgo\", \"title\": \"Observatoire global du Saint-Laurent\", \"type\": \"organization\", \"description\": \"\", \"image_url\": \"\", \"created\": \"2026-07-31T15:58:21.306495\", \"is_organization\": true, \"approval_status\": \"approved\", \"state\": \"active\", \"description_translated\": {\"en\": \"Created in 2005 by federal and provincial government as well as academic institutions and community organizations, the St. Lawrence Global Observatory (SLGO) makes it possible to maximize the benefits of data collection by integrating multidisciplinary data from multiple partners on a single web portal. Promoting data discovery and re-use, SLGO counts 48 members and is recognized throughout the world.\\r\\n\\r\\nThe content distributed by SLGO spans across all disciplines, themes and areas of interest that data-producing members choose to make accessible. A large amount of scientific and environmental information is already available through SLGO's portal. Furthermore, in order to maximize data availability, SLGO's team develops user-friendly web applications to facilitate data visualization and download in various formats.\\r\\n\\r\\nSLGO is, as such, responsible for the activities of the region of the St. Lawrence of CIOOS. To contribute, we invite you to contact us.\", \"fr\": \"Cr\\u00e9\\u00e9 en 2005 par un regroupement d\\u2019organisations provenant du gouvernement f\\u00e9d\\u00e9ral et provincial, du milieu acad\\u00e9mique et communautaire, l\\u2019Observatoire global du Saint-Laurent permet de maximiser les retomb\\u00e9es de la collecte de donn\\u00e9es par l\\u2019int\\u00e9gration de donn\\u00e9es multidisciplinaires provenant de multiples partenaires sur un portail web unique. Favorisant la d\\u00e9couverte des donn\\u00e9es et leur valorisation, l\\u2019OGSL compte actuellement 48 membres et est reconnu \\u00e0 travers le monde.\\r\\n\\r\\nLe contenu diffus\\u00e9 par l'OGSL couvre l'ensemble des disciplines, th\\u00e8mes et domaines d'int\\u00e9r\\u00eat que les membres producteurs de donn\\u00e9es choisissent de rendre accessibles. Une grande quantit\\u00e9 d'information de nature scientifique et environnementale est d\\u00e9j\\u00e0 disponible sur le portail de l'OGSL. De plus, l'\\u00e9quipe de l'OGSL d\\u00e9veloppe des applications web conviviales pour faciliter la visualisation et le t\\u00e9l\\u00e9chargement des donn\\u00e9es sous diff\\u00e9rents formats afin de maximiser la d\\u00e9mocratisation des donn\\u00e9es.\\r\\n\\r\\nL'OGSL est donc responsable des activit\\u00e9s de la r\\u00e9gion du Saint-Laurent du SIOOC. Pour contribuer, nous vous invitons \\u00e0 nous contacter.\"}, \"display_name\": \"St. Lawrence Global Observatory\", \"external_home_url\": \"https://ogsl.ca\", \"image_display_url\": \"\", \"image_url_translated\": {\"en\": \"https://ogsl.ca/wp_ogsl/logo_partenaires/OGSL_Logo.png\", \"fr\": \"https://ogsl.ca/wp_ogsl/logo_partenaires/OGSL_Logo.png\"}, \"num_followers\": 0, \"title_translated\": {\"en\": \"St. Lawrence Global Observatory\", \"fr\": \"Observatoire global du Saint-Laurent\"}, \"organization-uri\": [{\"authority\": \"\", \"code\": \"\", \"code-space\": \"\", \"version\": \"\"}]}"},{"key":"harvest_source_title","value":"St. Lawrence Global Observatory"},{"key":"legal-constraints-reference-code","value":"government-open-license-canada"},{"key":"licence","value":""},{"key":"metadata-date","value":"2025-02-14T18:27:43.921Z"},{"key":"metadata_created_source","value":"2023-05-18T14:39:24.556008"},{"key":"metadata_modified_source","value":"2025-02-14T18:30:48.245291"},{"key":"responsible-party","value":"[{\"name\": \"Fisheries and Oceans Canada\", \"roles\": [\"owner\", \"author\", \"pointOfContact\", \"collaborator\", \"custodian\", \"distributor\"]}]"},{"key":"spatial_harvester","value":"true"},{"key":"uri","value":"https://catalogue.ogsl.ca/dataset/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea"},{"key":"use-constraints-code","value":"licence"},{"key":"xml_modified_date","value":"2025-02-14 18:30:00"}],"groups":[{"id":"732f6694-3249-4d70-a1eb-bdb5838802ef","name":"resorg_fisheries-and-oceans-canada","type":"resorg","state":"active","title":"Pêches et Océans Canada","created":"2026-07-31T16:11:25.487962","group-uri":[{"code":"https://ror.org/02qa1x782","version":"","authority":"","code-space":""}],"image_url":"","description":"","display_name":"Pêches et Océans Canada","num_followers":0,"approval_status":"approved","is_organization":false,"title_translated":{"en":"Fisheries and Oceans Canada","fr":"Pêches et Océans Canada"},"external_home_url":"https://www.dfo-mpo.gc.ca","image_display_url":"","image_url_translated":{"en":"https://www.canada.ca/etc/designs/canada/wet-boew/assets/sig-blk-en.svg","fr":"https://www.canada.ca/etc/designs/canada/wet-boew/assets/sig-blk-en.svg"},"description_translated":{"en":"","fr":""}}],"isopen":false,"private":false,"spatial":{"type":"Polygon","coordinates":[[[-69.1,48.59],[-69.09,48.75],[-68.95,48.84],[-68.75,48.91],[-68.57,49.04],[-68.29,49.17],[-67.73,49.31],[-67.33,49.42],[-67.25,49.34],[-67.25,49.24],[-68.07,48.93],[-68.67,48.71],[-69.0,48.6],[-69.1,48.59]]]},"citation":{"en":"[{\\\"type\\\": \\\"dataset\\\", \\\"id\\\": \\\"ca.cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea\\\", \\\"author\\\": [{\\\"given\\\": \\\"Sandra\\\", \\\"family\\\": \\\"Velasquez\\\"}, {\\\"given\\\": \\\"Audrey\\\", \\\"family\\\": \\\"Bourret\\\"}, {\\\"given\\\": \\\"Yanick\\\", \\\"family\\\": \\\"Gendreau\\\"}, {\\\"literal\\\": \\\"Fisheries and Oceans Canada\\\"}], \\\"issued\\\": [{\\\"date-parts\\\": [\\\"2025\\\", \\\"02\\\", \\\"14\\\"]}], \\\"abstract\\\": \\\"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 invertebrate species whose DNA has been detected in water samples collected in 2018 using the mitochondrial marker COI.\\n\\nThe surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-C\\u00f4te-Nord) from the vessel CCGC Leim. 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 \\u00b5m 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 Gulf of St. Lawrence](https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) and a threshold of 40. Detections with an \\u201cUnreliable due to gaps'' category were reported at the genus level only.\\n\\nThe 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.\\n\\nThis project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline 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. Consult the dataset also available on the [**Open Data Canada**](https://ouvert.canada.ca/data/en/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a) portal.\\\", \\\"edition\\\": \\\"\\\", \\\"edition-date\\\": \\\"\\\", \\\"publisher\\\": \\\"\\\", \\\"title\\\": \\\"Use of the COI Marker for the Development of an Approach for Characterizing Coastal Species Using Environmental DNA (eDNA)\\\", \\\"DOI\\\": \\\"10.26071/ogsl-cd4c205b-f63b\\\", \\\"language\\\": \\\"en\\\", \\\"URL\\\": \\\"https://catalogue.ogsl.ca/dataset/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea?local=en\\\"}]","fr":"[{\\\"type\\\": \\\"dataset\\\", \\\"id\\\": \\\"ca.cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea\\\", \\\"author\\\": [{\\\"given\\\": \\\"Sandra\\\", \\\"family\\\": \\\"Velasquez\\\"}, {\\\"given\\\": \\\"Audrey\\\", \\\"family\\\": \\\"Bourret\\\"}, {\\\"given\\\": \\\"Yanick\\\", \\\"family\\\": \\\"Gendreau\\\"}, {\\\"literal\\\": \\\"Fisheries and Oceans Canada\\\"}], \\\"issued\\\": [{\\\"date-parts\\\": [\\\"2025\\\", \\\"02\\\", \\\"14\\\"]}], \\\"abstract\\\": \\\"La caract\\u00e9risation des esp\\u00e8ces par l\\u2019ADN environnemental (ADNe) est une m\\u00e9thode qui permet d\\u2019utiliser l\\u2019ADN lib\\u00e9r\\u00e9 dans l\\u2019environnement par les organismes de diverses sources (s\\u00e9cr\\u00e9tions, f\\u00e8ces, gam\\u00e8tes, tissus, etc.). C\\u2019est un outil compl\\u00e9mentaire aux m\\u00e9thodes standards d\\u2019\\u00e9chantillonnage pour l\\u2019identification de la biodiversit\\u00e9. Ce projet fournit une liste d\\u2019esp\\u00e8ces d\\u2019invert\\u00e9br\\u00e9s dont l\\u2019ADN a \\u00e9t\\u00e9 d\\u00e9tect\\u00e9 dans des \\u00e9chantillons d\\u2019eau collect\\u00e9s en 2018 \\u00e0 l\\u2019aide du marqueur COI.\\n\\nLe relev\\u00e9 a \\u00e9t\\u00e9 r\\u00e9alis\\u00e9 \\u00e0 l\\u2019\\u00e9t\\u00e9 2018 du 11 au 14 ao\\u00fbt, entre Forestville et Godbout (Haute-C\\u00f4te-Nord) \\u00e0 partir du navire NGCC Leim. L\\u2019\\u00e9chantillonnage a \\u00e9t\\u00e9 r\\u00e9alis\\u00e9 entre 9-52 m\\u00e8tres de profondeur dans 40 stations, avec un seul \\u00e9chantillon par station. Deux litres d\\u2019eau ont \\u00e9t\\u00e9 filtr\\u00e9s sur un filtre en fibre de verre de 1.2 \\u00b5m. Les extractions de l\\u2019ADN ont \\u00e9t\\u00e9 effectu\\u00e9es avec le kit d\\u2019extraction *DNeasy Blood and Tissue (Qiagen)*. Des contr\\u00f4les n\\u00e9gatifs de terrains, d\\u2019extractions et de PCR ont \\u00e9t\\u00e9 ajout\\u00e9s aux diff\\u00e9rentes \\u00e9tapes du protocole. Les librairies au locus COI ont \\u00e9t\\u00e9 pr\\u00e9par\\u00e9es par G\\u00e9nome Qu\\u00e9bec et s\\u00e9quenc\\u00e9es sur un syst\\u00e8me Illumina MiSeq PE250. L\\u2019analyse bio-informatique des s\\u00e9quences obtenues a \\u00e9t\\u00e9 r\\u00e9alis\\u00e9e \\u00e0 l\\u2019aide d\\u2019un pipeline d\\u2019analyse maison tel que rapport\\u00e9 dans Bourret et al. (2022). Une premi\\u00e8re \\u00e9tape a permis l\\u2019obtention d\\u2019une table d\\u2019unit\\u00e9 mol\\u00e9culaire op\\u00e9rationnelle de taxonomie (ou *Molecular operational taxonomic* unit, MOTU) \\u00e0 l\\u2019aide du logiciel Cutadapt pour le retrait des adaptateurs et du paquet R DADA2 pour la filtration, la fusion, le retrait des chim\\u00e8res et la compilation des donn\\u00e9es. La table de MOTUS a par la suite \\u00e9t\\u00e9 corrig\\u00e9e en prenant compte des t\\u00e9moins n\\u00e9gatifs, o\\u00f9 le nombre d\\u2019observations dans ces derniers a \\u00e9t\\u00e9 retir\\u00e9 des \\u00e9chantillons li\\u00e9s. Les MOTUs singletons ont \\u00e9galement \\u00e9t\\u00e9 retir\\u00e9s. Finalement, les assignations taxonomiques ont \\u00e9t\\u00e9 effectu\\u00e9es sur les MOTUs \\u00e0 l\\u2019aide du classificateur IDTAXA (pr\\u00e9sent dans le paquet R DECIPHIER) en utilisant un *training set* entra\\u00een\\u00e9 sur la [banque de r\\u00e9f\\u00e9rence COI pour le golfe du Saint-Laurent](https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) et un seuil de 40. Les d\\u00e9tections avec une cat\\u00e9gorie \\u00ab *Unreliable due to gaps* \\u00bb ont \\u00e9t\\u00e9 rapport\\u00e9es au niveau du genre uniquement. \\n\\nLes fichiers fournis comprennent les informations g\\u00e9n\\u00e9riques de l'activit\\u00e9, notamment le site, le nom de la station, la date, le type de marqueur, les types des assignations utilis\\u00e9es pour l\\u2019identification des taxons et une liste de taxons ou esp\\u00e8ces . La liste de taxons a \\u00e9t\\u00e9 v\\u00e9rifi\\u00e9e par un expert en biodiversit\\u00e9 de l'Institut Maurice-Lamontagne. \\n\\nCe projet a \\u00e9t\\u00e9 financ\\u00e9 par le Programme sur les donn\\u00e9es environnementales c\\u00f4ti\\u00e8res de r\\u00e9f\\u00e9rence de P\\u00eaches et Oc\\u00e9ans Canada dans le cadre du Plan de protection des oc\\u00e9ans. Cette initiative vise \\u00e0 acqu\\u00e9rir des donn\\u00e9es environnementales de base qui contribuent \\u00e0 la caract\\u00e9risation des zones c\\u00f4ti\\u00e8res d\\u2019importance et appuient des \\u00e9valuations fond\\u00e9es sur des preuves ainsi que les d\\u00e9cisions de gestion afin de pr\\u00e9server les \\u00e9cosyst\\u00e8mes marins. Consultez le jeu de donn\\u00e9es aussi disponible sur le portail de [**Donn\\u00e9es Ouvertes Canada**](https://ouvert.canada.ca/data/fr/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a).\\\", \\\"edition\\\": \\\"\\\", \\\"edition-date\\\": \\\"\\\", \\\"publisher\\\": \\\"\\\", \\\"title\\\": \\\"Utilisation du marqueur COI pour le d\\u00e9veloppement d\\u2019une approche de caract\\u00e9risation des esp\\u00e8ces c\\u00f4ti\\u00e8res \\u00e0 l\\u2019aide d\\u2019ADN environnemental (ADNe)\\\", \\\"DOI\\\": \\\"10.26071/ogsl-cd4c205b-f63b\\\", \\\"language\\\": \\\"fr\\\", \\\"URL\\\": \\\"https://catalogue.ogsl.ca/dataset/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea?local=fr\\\"}]"},"keywords":{"en":["Metabarcoding","fish","COI","Saint Lawrence River","Quebec","Invertebrate","eDNA","other","Animalia"],"fr":["Oceans","Metabarcoding","poisson","COI","Fleuve Saint-Laurent","Québec","Invertébré","ADNe","Autre","Animalia","Coastal Environmental Baseline Program"]},"num_tags":0,"progress":"completed","projects":["Coastal Environmental Baseline Program"],"owner_org":"b9a157db-ac56-4a28-aee9-899a35f463c6","resources":[{"id":"9bd32962-bd41-4715-bb05-6f568a8f6b87","url":"https://catalogue.ogsl.ca/data/dfo-mpo/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea/MetadonnéesCOI.csv","hash":"","name":"Métadonnées COI","size":null,"state":"active","format":"CSV","created":"2025-02-14T18:30:48.355565","mimetype":"text/csv","position":0,"url_type":null,"cache_url":null,"package_id":"27a6aea7-2c94-408e-a910-592c40d10083","description":"Fichier de métadonnées","last_modified":null,"resource_type":null,"created_source":"2025-02-14T18:30:48.355565","mimetype_inner":null,"name_translated":{"en":"Metadata COI","fr":"Métadonnées COI"},"datastore_active":false,"metadata_modified":"2026-07-31T16:34:44.282557","cache_last_updated":null,"description_translated":{"en":"Metadata files","fr":"Fichier de 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COI"},"datastore_active":false,"metadata_modified":"2026-07-31T16:34:44.285761","cache_last_updated":null,"description_translated":{"en":"Marker type, assignment types used for taxa identification, and a list of taxa or species","fr":"Types des assignations utilisées pour l’identification des taxons et une liste de taxons ou espèces"},"metadata_modified_source":"2025-02-14T18:30:48.263869","resource_locator_function":"","resource_locator_protocol":"WWW:LINK"}],"datacentre":[],"license_id":"government-open-license-canada","maintainer":null,"distributor":[{"role":["distributor"],"individual-name":"Velasquez, Sandra","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"Sandra.Velasquez@dfo-mpo.gc.ca","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""},{"role":["distributor"],"individual-name":"Gendreau, Yanick","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"Yanick.Gendreau@dfo-mpo.gc.ca","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""},{"role":["distributor"],"individual-name":"","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":""}],"author_email":null,"organization":{"id":"b9a157db-ac56-4a28-aee9-899a35f463c6","name":"slgo","type":"organization","state":"active","title":"Observatoire global du Saint-Laurent","created":"2026-07-31T15:58:21.306495","image_url":"","description":"","display_name":"St. Lawrence Global Observatory","num_followers":0,"approval_status":"approved","is_organization":true,"organization-uri":[{"code":"","version":"","authority":"","code-space":""}],"title_translated":{"en":"St. Lawrence Global Observatory","fr":"Observatoire global du Saint-Laurent"},"external_home_url":"https://ogsl.ca","image_display_url":"","image_url_translated":{"en":"https://ogsl.ca/wp_ogsl/logo_partenaires/OGSL_Logo.png","fr":"https://ogsl.ca/wp_ogsl/logo_partenaires/OGSL_Logo.png"},"description_translated":{"en":"Created in 2005 by federal and provincial government as well as academic institutions and community organizations, the St. Lawrence Global Observatory (SLGO) makes it possible to maximize the benefits of data collection by integrating multidisciplinary data from multiple partners on a single web portal. Promoting data discovery and re-use, SLGO counts 48 members and is recognized throughout the world.\r\n\r\nThe content distributed by SLGO spans across all disciplines, themes and areas of interest that data-producing members choose to make accessible. A large amount of scientific and environmental information is already available through SLGO's portal. Furthermore, in order to maximize data availability, SLGO's team develops user-friendly web applications to facilitate data visualization and download in various formats.\r\n\r\nSLGO is, as such, responsible for the activities of the region of the St. Lawrence of CIOOS. To contribute, we invite you to contact us.","fr":"Créé en 2005 par un regroupement d’organisations provenant du gouvernement fédéral et provincial, du milieu académique et communautaire, l’Observatoire global du Saint-Laurent permet de maximiser les retombées de la collecte de données par l’intégration de données multidisciplinaires provenant de multiples partenaires sur un portail web unique. Favorisant la découverte des données et leur valorisation, l’OGSL compte actuellement 48 membres et est reconnu à travers le monde.\r\n\r\nLe contenu diffusé par l'OGSL couvre l'ensemble des disciplines, thèmes et domaines d'intérêt que les membres producteurs de données choisissent de rendre accessibles. Une grande quantité d'information de nature scientifique et environnementale est déjà disponible sur le portail de l'OGSL. De plus, l'équipe de l'OGSL développe des applications web conviviales pour faciliter la visualisation et le téléchargement des données sous différents formats afin de maximiser la démocratisation des données.\r\n\r\nL'OGSL est donc responsable des activités de la région du Saint-Laurent du SIOOC. Pour contribuer, nous vous invitons à nous contacter."}},"license_title":"government-open-license-canada","num_resources":3,"resource-type":"dataset","bbox-east-long":"-67.25","bbox-north-lat":"48.59","bbox-south-lat":"49.42","bbox-west-long":"-69.1","creator_user_id":"fe6035ee-ed91-4ead-b5b2-4048232a22bb","temporal-extent":[{"end":"2018-08-14","begin":"2018-08-11"}],"vertical-extent":[{"max":"52.0","min":"9.0"}],"maintainer_email":null,"maintenance-note":"Generated from https://cioos-siooc.github.io/metadata-entry-form#/fr/stlaurent/QimW47K19EhGXEk1ZSN05cnKzxZ2/-NIEgfTeZQLFEBd3W8PQ","metadata_created":"2026-07-31T16:34:44.288739","notes_translated":{"en":"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 invertebrate species whose DNA has been detected in water samples collected in 2018 using the mitochondrial marker COI.\n\nThe surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord) from the vessel CCGC Leim. 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 Gulf of St. Lawrence](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.\n\nThe 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.\n\nThis project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline 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. Consult the dataset also available on the [**Open Data Canada**](https://ouvert.canada.ca/data/en/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a) portal.","fr":"La caractérisation des espèces par l’ADN environnemental (ADNe) est une méthode qui permet d’utiliser l’ADN libéré dans l’environnement par les organismes de diverses sources (sécrétions, fèces, gamètes, tissus, etc.). C’est un outil complémentaire aux méthodes standards d’échantillonnage pour l’identification de la biodiversité. Ce projet fournit une liste d’espèces d’invertébrés dont l’ADN a été détecté dans des échantillons d’eau collectés en 2018 à l’aide du marqueur COI.\n\nLe relevé a été réalisé à l’été 2018 du 11 au 14 août, entre Forestville et Godbout (Haute-Côte-Nord) à partir du navire NGCC Leim. L’échantillonnage a été réalisé entre 9-52 mètres de profondeur dans 40 stations, avec un seul échantillon par station. Deux litres d’eau ont été filtrés sur un filtre en fibre de verre de 1.2 µm. Les extractions de l’ADN ont été effectuées avec le kit d’extraction *DNeasy Blood and Tissue (Qiagen)*. Des contrôles négatifs de terrains, d’extractions et de PCR ont été ajoutés aux différentes étapes du protocole. Les librairies au locus COI ont été préparées par Génome Québec et séquencées sur un système Illumina MiSeq PE250. L’analyse bio-informatique des séquences obtenues a été réalisée à l’aide d’un pipeline d’analyse maison tel que rapporté dans Bourret et al. (2022). Une première étape a permis l’obtention d’une table d’unité moléculaire opérationnelle de taxonomie (ou *Molecular operational taxonomic* unit, MOTU) à l’aide du logiciel Cutadapt pour le retrait des adaptateurs et du paquet R DADA2 pour la filtration, la fusion, le retrait des chimères et la compilation des données. La table de MOTUS a par la suite été corrigée en prenant compte des témoins négatifs, où le nombre d’observations dans ces derniers a été retiré des échantillons liés. Les MOTUs singletons ont également été retirés. Finalement, les assignations taxonomiques ont été effectuées sur les MOTUs à l’aide du classificateur IDTAXA (présent dans le paquet R DECIPHIER) en utilisant un *training set* entraîné sur la [banque de référence COI pour le golfe du Saint-Laurent](https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) et un seuil de 40. Les détections avec une catégorie « *Unreliable due to gaps* » ont été rapportées au niveau du genre uniquement. \n\nLes fichiers fournis comprennent les informations génériques de l'activité, notamment le site, le nom de la station, la date, le type de marqueur, les types des assignations utilisées pour l’identification des taxons et une liste de taxons ou espèces . La liste de taxons a été vérifiée par un expert en biodiversité de l'Institut Maurice-Lamontagne. \n\nCe projet a été financé par le Programme sur les données environnementales côtières de référence de Pêches et Océans Canada dans le cadre du Plan de protection des océans. Cette initiative vise à acquérir des données environnementales de base qui contribuent à la caractérisation des zones côtières d’importance et appuient des évaluations fondées sur des preuves ainsi que les décisions de gestion afin de préserver les écosystèmes marins. Consultez le jeu de données aussi disponible sur le portail de [**Données Ouvertes Canada**](https://ouvert.canada.ca/data/fr/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a)."},"title_translated":{"en":"Use of the COI Marker for the Development of an Approach for Characterizing Coastal Species Using Environmental DNA (eDNA)","fr":"Utilisation du marqueur COI pour le développement d’une approche de caractérisation des espèces côtières à l’aide d’ADN environnemental (ADNe)"},"xml_location_url":"https://catalogue-waf.ogsl.ca/metadata-files/dfo-mpo/cd4c205b-f63b-4d2f-92bf-77fb89fc9eea.xml","metadata-language":"fr","metadata_modified":"2026-07-31T16:34:44.288744","frequency-of-update":"asNeeded","dataset-reference-date":[{"type":"creation","value":"2018-08-11"}],"cited-responsible-party":[{"role":["author","custodian","distributor","owner","pointOfContact","collaborator"],"individual-name":"Velasquez, Sandra","organisation-name":"Fisheries and Oceans 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Canada","contact-info_email":"Yanick.Gendreau@dfo-mpo.gc.ca","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""},{"role":["distributor","owner"],"individual-name":"","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":""}],"metadata-reference-date":[{"type":"publication","value":"2023-02-01"},{"type":"revision","value":"2025-02-14"}],"relationships_as_object":[],"harvest_document_content":"\n \n \n \n \n \n ca.cioos\n \n \n \n \n cd4c205b-f63b-4d2f-92bf-77fb89fc9eea\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n gddaiss-dmsaisb@dfo-mpo.gc.ca\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Section, Data Management\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n gddaiss-dmsaisb@dfo-mpo.gc.ca\n \n \n \n \n \n \n Gestionnaire de données\n \n \n \n \n \n \n \n \n \n \n 2025-02-14T18:27:43.921Z\n \n \n revision\n \n \n \n \n \n \n 2023-02-01\n \n \n publication\n \n \n \n \n \n \n ISO 19115-1 Geographic information - Metadata\n \n \n First Edition 2014-04-01\n \n \n \n \n \n \n ISO 19115-2 Geographic information - Metadata\n \n \n Second Edition 2019-01\n \n \n \n \n \n \n ISO 19115-1 Geographic Information - Metadata Amendment 1\n \n \n 2018-02\n \n \n \n \n \n \n Canadian Integrated Ocean Observing System Metadata Profile of ISO 19115\n \n \n \n \n 2019-11-06\n \n \n publication\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Utilisation du marqueur COI pour le développement d’une approche de caractérisation des espèces côtières à l’aide d’ADN environnemental (ADNe)\n \n \n Use of the COI Marker for the Development of an Approach for Characterizing Coastal Species Using Environmental DNA (eDNA)\n \n \n \n \n \n \n 2018-08-11\n \n \n creation\n \n \n \n \n \n \n https://doi.org/10.26071/ogsl-cd4c205b-f63b\n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Bourret, Audrey\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Audrey.bourret@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Bourret, Audrey\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Audrey.bourret@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n \n \n \n \n La caractérisation des espèces par l’ADN environnemental (ADNe) est une méthode qui permet d’utiliser l’ADN libéré dans l’environnement par les organismes de diverses sources (sécrétions, fèces, gamètes, tissus, etc.). C’est un outil complémentaire aux méthodes standards d’échantillonnage pour l’identification de la biodiversité. Ce projet fournit une liste d’espèces d’invertébrés dont l’ADN a été détecté dans des échantillons d’eau collectés en 2018 à l’aide du marqueur COI.\n\nLe relevé a été réalisé à l’été 2018 du 11 au 14 août, entre Forestville et Godbout (Haute-Côte-Nord) à partir du navire NGCC Leim. L’échantillonnage a été réalisé entre 9-52 mètres de profondeur dans 40 stations, avec un seul échantillon par station. Deux litres d’eau ont été filtrés sur un filtre en fibre de verre de 1.2 µm. Les extractions de l’ADN ont été effectuées avec le kit d’extraction *DNeasy Blood and Tissue (Qiagen)*. Des contrôles négatifs de terrains, d’extractions et de PCR ont été ajoutés aux différentes étapes du protocole. Les librairies au locus COI ont été préparées par Génome Québec et séquencées sur un système Illumina MiSeq PE250. L’analyse bio-informatique des séquences obtenues a été réalisée à l’aide d’un pipeline d’analyse maison tel que rapporté dans Bourret et al. (2022). Une première étape a permis l’obtention d’une table d’unité moléculaire opérationnelle de taxonomie (ou *Molecular operational taxonomic* unit, MOTU) à l’aide du logiciel Cutadapt pour le retrait des adaptateurs et du paquet R DADA2 pour la filtration, la fusion, le retrait des chimères et la compilation des données. La table de MOTUS a par la suite été corrigée en prenant compte des témoins négatifs, où le nombre d’observations dans ces derniers a été retiré des échantillons liés. Les MOTUs singletons ont également été retirés. Finalement, les assignations taxonomiques ont été effectuées sur les MOTUs à l’aide du classificateur IDTAXA (présent dans le paquet R DECIPHIER) en utilisant un *training set* entraîné sur la [banque de référence COI pour le golfe du Saint-Laurent](https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) et un seuil de 40. Les détections avec une catégorie « *Unreliable due to gaps* » ont été rapportées au niveau du genre uniquement. \n\nLes fichiers fournis comprennent les informations génériques de l'activité, notamment le site, le nom de la station, la date, le type de marqueur, les types des assignations utilisées pour l’identification des taxons et une liste de taxons ou espèces . La liste de taxons a été vérifiée par un expert en biodiversité de l'Institut Maurice-Lamontagne. \n\nCe projet a été financé par le Programme sur les données environnementales côtières de référence de Pêches et Océans Canada dans le cadre du Plan de protection des océans. Cette initiative vise à acquérir des données environnementales de base qui contribuent à la caractérisation des zones côtières d’importance et appuient des évaluations fondées sur des preuves ainsi que les décisions de gestion afin de préserver les écosystèmes marins. Consultez le jeu de données aussi disponible sur le portail de [**Données Ouvertes Canada**](https://ouvert.canada.ca/data/fr/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a).\n \n \n 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 invertebrate species whose DNA has been detected in water samples collected in 2018 using the mitochondrial marker COI.\n\nThe surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord) from the vessel CCGC Leim. 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 Gulf of St. Lawrence](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.\n\nThe 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.\n\nThis project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline 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. Consult the dataset also available on the [**Open Data Canada**](https://ouvert.canada.ca/data/en/dataset/6319d10d-2ea7-44af-bfde-20e2da053d5a) portal.\n \n \n \n \n \n \n \n \n \n \n oceans\n \n \n \n \n \n \n true\n \n \n \n \n \n -69.10,48.59 -69.09,48.75 -68.95,48.84 -68.75,48.91 -68.57,49.04 -68.29,49.17 -67.73,49.31 -67.33,49.42 -67.25,49.34 -67.25,49.24 -68.07,48.93 -68.67,48.71 -69.00,48.60 -69.10,48.59\n \n \n \n \n \n \n \n \n \n \n \n \n \n 9.0\n \n \n 52.0\n \n \n \n \n \n \n 5829\n \n \n EPSG\n \n \n 2012-08-10\n \n \n EPSG::5829 - Instantaneous Water Level height - Height relative to instantaneous water level uncorrected for tide. Not specific to any location or epoch.\n \n \n \n \n vertical\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2018-08-11T16:00:00.000Z\n 2018-08-14T16:00:00.000Z\n \n \n \n \n \n \n \n \n \n asNeeded\n \n \n Generated from https://cioos-siooc.github.io/metadata-entry-form#/fr/stlaurent/QimW47K19EhGXEk1ZSN05cnKzxZ2/-NIEgfTeZQLFEBd3W8PQ\n \n \n \n \n \n \n Oceans\n \n \n \n \n Government of Canada Core Subject Thesaurus\n \n \n \n \n 2016-10-13\n \n \n \n \n \n \n \n N/A\n \n \n \n \n \n \n \n \n Metabarcoding\n \n \n poisson\n \n \n COI\n \n \n Fleuve Saint-Laurent\n \n \n Québec\n \n \n Invertébré\n \n \n ADNe\n \n \n \n \n Metabarcoding\n \n \n \n \n \n \n fish\n \n \n \n \n \n \n COI\n \n \n \n \n \n \n Saint Lawrence River\n \n \n \n \n \n \n Quebec\n \n \n \n \n \n \n Invertebrate\n \n \n \n \n \n \n eDNA\n \n \n \n \n \n \n default\n \n \n \n \n \n \n \n \n Autre\n \n \n \n \n other\n \n \n \n \n \n \n eov\n \n \n \n \n \n \n \n \n Animalia\n \n \n \n \n Animalia\n \n \n \n \n \n \n taxa\n \n \n \n \n \n \n \n \n Coastal Environmental Baseline Program\n \n \n project\n \n \n \n \n \n \n \n \n Licence du gouvernement ouvert – Canada \n \n \n Open Government Licence - Canada\n \n \n \n \n \n \n government-open-license-canada\n \n \n \n \n \n \n https://open.canada.ca/en/open-government-licence-canada\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Velasquez, Sandra\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Sandra.Velasquez@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste en Sciences aquatiques\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n Gendreau, Yanick\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Yanick.Gendreau@dfo-mpo.gc.ca\n \n \n \n \n \n \n Biologiste\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Fisheries and Oceans Canada\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Ottawa\n \n \n Canada\n \n \n \n \n \n \n http://www.dfo-mpo.gc.ca/index-eng.htm\n \n \n WWW:LINK\n \n \n \n \n \n \n \n \n \n \n \n https://ror.org/02qa1x782\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n https://catalogue.ogsl.ca/data/dfo-mpo/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea/MetadonnéesCOI.csv\n \n \n WWW:LINK\n \n \n Métadonnées COI\n \n \n Metadata COI\n \n \n \n \n Fichier de métadonnées\n \n \n Metadata files\n \n \n \n \n \n \n \n \n \n \n \n \n https://catalogue.ogsl.ca/data/dfo-mpo/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea/Dictionnaire_de_vocabulaire.pdf\n \n \n WWW:LINK\n \n \n Dictionnaire de vocabulaire\n \n \n Vocabulary dictionnary\n \n \n \n \n Dictionnaire de variable détaillant chaque variable\n \n \n Variable dictionary detailing each variable\n \n \n \n \n \n \n \n \n \n \n \n \n https://catalogue.ogsl.ca/data/dfo-mpo/ca-cioos_cd4c205b-f63b-4d2f-92bf-77fb89fc9eea/Assignations_COI.csv\n \n \n WWW:LINK\n \n \n Assignations marqueur COI\n \n \n COI marker assignments\n \n \n \n \n Types des assignations utilisées pour l’identification des taxons et une liste de taxons ou espèces\n \n \n Marker type, assignment types used for taxa identification, and a list of taxa or species\n \n \n \n \n \n \n \n \n \n \n \n \n asNeeded\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 18LO\n \n \n \n \n NGCC Leim\n \n \n CCGS Leim\n \n \n \n \n \n \n research vessel\n \n \n \n \n \n \n","notes_translation_method":{"en":"","fr":""},"relationships_as_subject":[],"title_translation_method":{"en":"","fr":""},"metadata-point-of-contact":[{"role":["author","custodian","distributor","owner","pointOfContact","collaborator"],"individual-name":"Velasquez, Sandra","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"Sandra.Velasquez@dfo-mpo.gc.ca","individual-uri_code":"","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""},{"role":["author","custodian","distributor","owner","collaborator"],"individual-name":"Gendreau, Yanick","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"Yanick.Gendreau@dfo-mpo.gc.ca","individual-uri_code":"","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""},{"role":"pointOfContact","individual-name":"Section, Data Management","organisation-name":"Fisheries and Oceans Canada","contact-info_email":"gddaiss-dmsaisb@dfo-mpo.gc.ca","individual-uri_code":"","organisation-uri_code":"https://ror.org/02qa1x782","organisation-uri_version":"","organisation-uri_authority":"","organisation-uri_code-space":"","contact-info_online-resource":""}],"included_in_data_catalogue":[{"url":"https://catalogue.juno.cioos.ca","name":{"en":"CIOOS Catalogue","fr":"Catalogue du SIOOC"},"description":""},{"url":"https://catalogue.ogsl.ca","name":"OGSL/SLGO","description":""}],"keywords_translation_method":{"fr":""},"unique-resource-identifier-full":[{"code":"https://doi.org/10.26071/ogsl-cd4c205b-f63b","version":"","authority":"","code-space":""}]}}