Catalogue PIGMA
Metabarcoding of pelagic communities in french's marinas
Simple
- Date (Creation)
- 2023-01-04
- Date (Publication)
- 2024-01-29
- Identifier
- FR-330-715-368-00032-IFR_BIOINFO_MTB_MarEEE_1_20230320_MARBEC_AC
Identifier
- Credit
- IFREMER (MARBEC/LEGPM) and CNRS ISEM
04 99 57 32 95
- GEMET - INSPIRE themes, version 1.0
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- Habitats and biotopes
- Thèmes Sextant
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- /Biological Environment/Bioinformatics
- ODATIS aggregation parameters and Essential Variable names
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- Bioinformatics
- Use limitation
- CC0 (Creative Commons - Transfer into public domain)
- Access constraints
- License
- Use constraints
- License
- Spatial representation type
- grid Grid
- Metadata language
- English
- Character set
- utf8 UTF8
- Topic category
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- Oceans
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- Reference system identifier
- EPSG / WGS 84 (EPSG:4326) / 8.6
Spatial representation info
- Distribution format
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- OnLine resource
- /home/ref-bioinfo/ifremer/marbec/marEEE ( NETWORK:LINK )
- OnLine resource
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Brandt, M. I., B. Trouche, L. Quintric, B. Gunther, P. Wincker, J. Poulain, and S. Arnaud-Haond. 2021. Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding. Mol Ecol Resour 21:1904-1921
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WWW:LINK
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Brandt, M. I., B. Trouche, L. Quintric, B. Gunther, P. Wincker, J. Poulain, and S. Arnaud-Haond. 2021. Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding. Mol Ecol Resour 21:1904-1921
- OnLine resource
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Couton, M., Baud, A., Daguin‐Thiébaut, C., Corre, E., Comtet, T., & Viard, F. 2021. High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally. Ecology and Evolution. doi:10.1002/ece3.7453
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WWW:LINK
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Couton, M., Baud, A., Daguin‐Thiébaut, C., Corre, E., Comtet, T., & Viard, F. 2021. High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally. Ecology and Evolution. doi:10.1002/ece3.7453
- OnLine resource
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Couton, M., Lévêque, L., Daguin-Thiébaut, C., Comtet, T., & Viard, F. 2022. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. Biofouling, 38(4), 367-383. doi:10.1080/08927014.2022.2075739
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WWW:LINK
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Couton, M., Lévêque, L., Daguin-Thiébaut, C., Comtet, T., & Viard, F. 2022. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. Biofouling, 38(4), 367-383. doi:10.1080/08927014.2022.2075739
- OnLine resource
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Leray, M., Yang, J.Y., Meyer, C.P. et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool 10, 34 (2013). https://doi.org/10.1186/1742-9994-10-34
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WWW:LINK
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Leray, M., Yang, J.Y., Meyer, C.P. et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool 10, 34 (2013). https://doi.org/10.1186/1742-9994-10-34
- OnLine resource
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Sinniger, F., J. Pawlowski, S. Harii, A. J. Gooday, H. Yamamoto, P. Chevaldonné, T. Cedhagen, G. Carvalho, and S. Creer. 2016. Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Frontiers in Marine Science 3. https://doi.org/10.3389/fmars.2016.00092
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WWW:LINK
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Sinniger, F., J. Pawlowski, S. Harii, A. J. Gooday, H. Yamamoto, P. Chevaldonné, T. Cedhagen, G. Carvalho, and S. Creer. 2016. Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Frontiers in Marine Science 3. https://doi.org/10.3389/fmars.2016.00092
- Hierarchy level
- Dataset
- Statement
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Metabarcoding data including 18S, 12S COI of environmental samples collected within and outside french's marinas of the mediterannean and the Atlantic.
DNA samples were obtained by seawater filtration collected in each marina followed by extraction of environmental DNA following the protocol detailed in Couton et al. (2022), and on the other hand by scraping boat hulls followed by extraction of DNA contained in the preservative alcohol of the resulting specimen mixtures ('bulk') following the protocol detailed in Couton et al. (2021).
Based on these DNAs, metabarcode libraries were built for three gene fragments: Cytochrome Oxidase I (Leray et al., 2013), 18S rDNA V1-V2 (Sinninger et al., 2016) and 12S rDNA (Taberlet, pers. comm.). These metabarcode libraries were sequenced on NovaSeq 6000. Data analyzes were carried out following the eDNAbyss pipeline (Brandt et al., 2021) available under Gitlab (https://gitlab.ifremer.fr/abyss-project/ ) to get the ASVs and OTUs tables.
Data obtained within the framework of the MarEEE project: “Cross-views on port marine environments: ecology-evolution-economy” (2020-2023); funded by the ANR-Investissements d’Avenir (i-site MUSE ; ANR-16-IDEX-006) and the project “Réseau Alien Occitanie” (CPIE-Bassin de Thau).
The data presented here are those acquired as part of Theme 1 of the project: study of communities by metabarcoding of environmental DNA from water samples filtered in marinas and at their entrances, and DNA from mixtures of species collected during the careening of boat hulls.
- File identifier
- 9dbe4e09-5411-4820-8040-55fbc6af378a XML
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2025-05-15T23:29:52.227419Z
- Metadata standard name
- ISO 19115-3 - SEXTANT
- Metadata standard version
- 1.0
04 99 57 32 95
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