Title

Metabarcoding of pelagic communities in french's marinas

Date (Creation)

2023-01-04

Date (Publication)

2024-01-29

Citation identifier

FR-330-715-368-00032-IFR_BIOINFO_MTB_MarEEE_1_20230320_MARBEC_AC

Abstract

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.

Credit

IFREMER (MARBEC/LEGPM) and CNRS ISEM

Point of contact

Organisation name	Individual name	Electronic mail address	Role
IFREMER		sismer@ifremer.fr	Publisher
IFREMER	Arnaud-Haond Sophie	Sophie.Arnaud@ifremer.fr	Author
CNRS Sorbonne Université	Ballenghien Marion	mballenghien@sb-roscoff.fr	Author
IFREMER	Bouchoucha Marc	marc.bouchoucha@ifremer.fr	Author
Université de Montpellier	Caillarec-Joly Annaëlle	annaelle.joly@umontpellier.fr	Author
CNRS Sorbonne Université	Comtet Thierry	comtet@sb-roscoff.fr	Author
CNRS	Viard Frédérique	frederique.viard@umontpellier.fr	Author
CNRS	Plateform Genseq	genseq-contact@umontpellier.fr	Author

GEMET - INSPIRE themes, version 1.0

• Habitats and biotopes

Thèmes Sextant

• /Biological Environment/Bioinformatics

ODATIS aggregation parameters and Essential Variable names

• Bioinformatics

Use limitation

CC0 (Creative Commons - Transfer into public domain)

Access constraints

License

Use constraints

License

Spatial representation type

Grid

Language

English

Character set

UTF8

Topic category

• Oceans

Reference system identifier

EPSG / WGS 84 (EPSG:4326) / 8.6

Distribution format

Name	Version

OnLine resource

Protocol	Linkage	Name
NETWORK:LINK	/home/ref-bioinfo/ifremer/marbec/marEEE
WWW:LINK-1.0-http--link	https://doi.org/10.1111/1755-0998.13398	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
WWW:LINK	https://doi.org/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
WWW:LINK	https://doi.org/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
WWW:LINK	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
WWW:LINK	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

Hierarchy level

Dataset

Statement

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.

Metadata

File identifier

9dbe4e09-5411-4820-8040-55fbc6af378a

Metadata language

English

Character set

UTF8

Hierarchy level

Dataset

Date stamp

2024-01-29T14:15:11.896Z

Metadata standard name

ISO 19115:2003/19139 - SEXTANT

Metadata standard version

1.0

Metadata author

Organisation name	Individual name	Electronic mail address	Role
IFREMER	Arnaud-Haond Sophie	Sophie.Arnaud@ifremer.fr	Local service desk