The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (euka2 data)

This dataset is associated to the following publication: Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, e17373. https://doi.org/10.1111/mec.17373

It contains the data obtained with the euka2 marker:

fastq files are the raw NGS eDNA sequencing outputs

dat file records the adapters names and oligos used for sequencing

Metadata associated to each eDNA sample are also provided.

Methods

eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France).

References

Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE, 10(10), e0139633. https://doi.org/10.1371/journal.pone.0139633

Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444

Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140

Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press.

Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428