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2026
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| Online Access: | https://doi.org/10.5281/zenodo.19632267 |
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| author | Macé, Bastien Manel, Stéphanie Delrieu-Trottin, Erwan Bruno, Morgane Valentini, Alice Mouillot, David Velez, Laure Avouac, Amandine Orblin, Marie Deter, Julie Bockel, Thomas Boissery, Pierre Le Roux, Gwénolé |
| author_facet | Macé, Bastien Manel, Stéphanie Delrieu-Trottin, Erwan Bruno, Morgane Valentini, Alice Mouillot, David Velez, Laure Avouac, Amandine Orblin, Marie Deter, Julie Bockel, Thomas Boissery, Pierre Le Roux, Gwénolé |
| contents | <p>This dataset is associated to the following publication: <strong>Macé, B.</strong>, Delrieu-Trottin, E., Mouillot, D., Valentini, A., Bruno, M., Velez, L., Avouac, A., Deter, J., Bockel, T., Orblin, M., Boissery, P., Le Roux, G., & Manel, S. (<strong>2026</strong>). Cities at sea: Coastal urbanization generates local biodiversity hotspots but regional coldspots in marine communities.</p> <p>It contains the raw eDNA metabarcoding data (part 4/5): the <em>all_samples.csv</em> file records the corresponding sample for each position of the sequencing plate, and the <em>.fastq</em> files are the raw NGS eDNA sequencing outputs.</p> <p> </p> <p><strong>Methods</strong></p> <blockquote> <p>DNA extraction, amplification, and sequencing were conducted following a previously described protocol (Pichot et al., 2025). Briefly, two independent extractions per sample were carried out alongside negative extraction controls to monitor potential contamination using the NucleoSpin® Soil kit (Macherey-Nagel, Germany), and the two extracts per sample were pooled. PCR amplifications were performed using the teleo primer pair (Valentini et al., 2016), targeting a ~60 bp fragment of the 12S mitochondrial DNA region in fish (teleosts and elasmobranchs). Twelve PCR replicates per sample were run, each with a unique eight nucleotide tag for downstream identification (identical tag for both the forward and the reverse primer). Negative PCR controls were analyzed in parallel. Amplified products were quantified, purified, and pooled to reach a theoretical depth of 1,000,000 reads per sample before library preparation. High-throughput sequencing libraries were prepared using the TruSeq® DNA PCR-Free kit (Illumina, USA) and sequenced on a NextSeq® 1000 (Illumina) using a P1 or P2 kit (Illumina).</p> </blockquote> <p> </p> <p><strong>References</strong></p> <p>Pichot, F., Manel, S., Velez, L., Juhel, J.-B., Ballesta, L., Boissery, P., Bruno, M., Cancemi, M., Holon, F., Riutort, J.-J., Schultz, M., Tomasi, N., Valentini, A., Adam, O., Deter, J., & Mouillot, D. (2025). Mesophotic protected habitats as refugia for the most at-risk elasmobranch species. <em>Biological Conservation</em>, <em>310</em>, 111371. https://doi.org/10.1016/j.biocon.2025.111371</p> <p>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. <em>Molecular Ecology</em>, <em>25</em>(4), 929–942. https://doi.org/10.1111/mec.13428</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19632267 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Cities at sea: Coastal urbanization generates local biodiversity hotspots but regional coldspots in marine communities (metabarcoding raw data 5/5) Macé, Bastien Manel, Stéphanie Delrieu-Trottin, Erwan Bruno, Morgane Valentini, Alice Mouillot, David Velez, Laure Avouac, Amandine Orblin, Marie Deter, Julie Bockel, Thomas Boissery, Pierre Le Roux, Gwénolé <p>This dataset is associated to the following publication: <strong>Macé, B.</strong>, Delrieu-Trottin, E., Mouillot, D., Valentini, A., Bruno, M., Velez, L., Avouac, A., Deter, J., Bockel, T., Orblin, M., Boissery, P., Le Roux, G., & Manel, S. (<strong>2026</strong>). Cities at sea: Coastal urbanization generates local biodiversity hotspots but regional coldspots in marine communities.</p> <p>It contains the raw eDNA metabarcoding data (part 4/5): the <em>all_samples.csv</em> file records the corresponding sample for each position of the sequencing plate, and the <em>.fastq</em> files are the raw NGS eDNA sequencing outputs.</p> <p> </p> <p><strong>Methods</strong></p> <blockquote> <p>DNA extraction, amplification, and sequencing were conducted following a previously described protocol (Pichot et al., 2025). Briefly, two independent extractions per sample were carried out alongside negative extraction controls to monitor potential contamination using the NucleoSpin® Soil kit (Macherey-Nagel, Germany), and the two extracts per sample were pooled. PCR amplifications were performed using the teleo primer pair (Valentini et al., 2016), targeting a ~60 bp fragment of the 12S mitochondrial DNA region in fish (teleosts and elasmobranchs). Twelve PCR replicates per sample were run, each with a unique eight nucleotide tag for downstream identification (identical tag for both the forward and the reverse primer). Negative PCR controls were analyzed in parallel. Amplified products were quantified, purified, and pooled to reach a theoretical depth of 1,000,000 reads per sample before library preparation. High-throughput sequencing libraries were prepared using the TruSeq® DNA PCR-Free kit (Illumina, USA) and sequenced on a NextSeq® 1000 (Illumina) using a P1 or P2 kit (Illumina).</p> </blockquote> <p> </p> <p><strong>References</strong></p> <p>Pichot, F., Manel, S., Velez, L., Juhel, J.-B., Ballesta, L., Boissery, P., Bruno, M., Cancemi, M., Holon, F., Riutort, J.-J., Schultz, M., Tomasi, N., Valentini, A., Adam, O., Deter, J., & Mouillot, D. (2025). Mesophotic protected habitats as refugia for the most at-risk elasmobranch species. <em>Biological Conservation</em>, <em>310</em>, 111371. https://doi.org/10.1016/j.biocon.2025.111371</p> <p>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. <em>Molecular Ecology</em>, <em>25</em>(4), 929–942. https://doi.org/10.1111/mec.13428</p> |
| title | Cities at sea: Coastal urbanization generates local biodiversity hotspots but regional coldspots in marine communities (metabarcoding raw data 5/5) |
| url | https://doi.org/10.5281/zenodo.19632267 |