9dbe4e09-5411-4820-8040-55fbc6af378a Arnaud-Haond Sophie IFREMER 04 99 57 32 61 04 99 57 32 95 Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sete France Sophie.Arnaud@ifremer.fr pointOfContact 2025-12-13T16:02:13.115005Z ISO 19115-3 - SEXTANT 1.0 WGS 84 (EPSG:4326) EPSG 8.6 Metabarcoding of pelagic communities in french's marinas 2023-01-04 creation 2024-01-29 publication FR-330-715-368-00032-IFR_BIOINFO_MTB_MarEEE_1_20230320_MARBEC_AC Metabarcoding data were produced based on samples gathered at Ifremer where the DNA was extracted; PCR libraries were built at Ifremer and Genseq; libraries were sequenced at Novogene. The data to download contain: 1/d emultiplexed raw data, 2/ metadata, and 3) Scripts to process data and taxonomically assign DNA sequences 4) Rmarkdown to analyze communities. IFREMER (MARBEC/LEGPM) and CNRS ISEM IFREMER sismer@ifremer.fr publisher Arnaud-Haond Sophie IFREMER 04 99 57 32 61 04 99 57 32 95 Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sete France Sophie.Arnaud@ifremer.fr author Ballenghien Marion CNRS Sorbonne Université mballenghien@sb-roscoff.fr author Bouchoucha Marc IFREMER marc.bouchoucha@ifremer.fr author Caillarec-Joly Annaëlle Université de Montpellier annaelle.joly@umontpellier.fr author Comtet Thierry CNRS Sorbonne Université comtet@sb-roscoff.fr author Viard Frédérique CNRS frederique.viard@umontpellier.fr author Plateform Genseq CNRS genseq-contact@umontpellier.fr author https://sextant.ifremer.fr/geonetwork/srv/api/records/9dbe4e09-5411-4820-8040-55fbc6af378a/attachments/1_LUZ_P8310040.jpg Habitats and biotopes GEMET - INSPIRE themes, version 1.0 2018-07-27T14:39:48 publication 2018-07-27 publication geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme /Biological Environment/Bioinformatics Thèmes Sextant 2025-12-09 publication geonetwork.thesaurus.local.theme.sextant-theme Bioinformatics ODATIS aggregation parameters and Essential Variable names 2025-07-29 publication geonetwork.thesaurus.external.theme.NVS.OD1 Analysis data Type de jeux de donnée ODATIS 2025-12-09 publication geonetwork.thesaurus.local.theme.type_jeux_donnee CC0 (Creative Commons - Transfer into public domain) grid utf8 oceans -6.00 10.00 40.00 50.40 /home/ref-bioinfo/ifremer/marbec/marEEE NETWORK:LINK https://doi.org/10.1111/1755-0998.13398 WWW:LINK 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 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 https://doi.org/10.1002/ece3.7453 WWW:LINK 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 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 https://doi.org/10.1080/08927014.2022.2075739 WWW:LINK 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 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 https://doi.org/10.1186/1742-9994-10-34 WWW:LINK 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 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 https://doi.org/10.3389/fmars.2016.00092 WWW:LINK 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 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 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.