Metabarcoding of pelagic communities in french's marinas
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.
| Data accessChemin d'accès | /home/ref-bioinfo/ifremer/marbec/marEEE |
| Date(s)Date(s) |
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| Author(s)Auteur(s) | Arnaud-Haond Sophie
(IFREMER)
Ballenghien Marion (CNRS Sorbonne Université) Bouchoucha Marc (IFREMER) Caillarec-Joly Annaëlle (Université de Montpellier) Comtet Thierry (CNRS Sorbonne Université) Viard Frédérique (CNRS) Plateform Genseq (CNRS) |
| Contact(s)Contact(s) | IFREMER
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| SourceSource |
IFREMER (MARBEC/LEGPM) and CNRS ISEM |
| LineageGénéalogie |
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. |
| ConstraintsContraintes |
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| Spatial informationsInformations géographiques |
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