The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (euka2 data)
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This dataset is associated to the following publication: Macé et al., 2024. 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 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
本数据集关联以下发表论文：Macé 等人，2024年。 本数据集包含使用euka2标记（euka2 marker）获取的实验数据： fastq格式文件为原始下一代测序（next-generation sequencing, NGS）环境DNA（environmental DNA, eDNA）测序产出文件；dat格式文件记录了测序所用的接头名称与寡核苷酸序列。 实验方法 环境DNA（eDNA）提取工作在专门用于eDNA样本的生物安全二级（BSL-2）实验室中开展，严格遵循Polanco Fernández等人（2021年）描述的实验流程。本研究采用覆盖生命全谱系的4组不同扩增体系，完成聚合酶链式反应（polymerase chain reaction, PCR）扩增：teleo引物对（Valentini等人，2016年）靶向硬骨鱼与软骨鱼的12S线粒体DNA标记位点；metazoa引物对（Kelly等人，2016年）靶向后生动物的16S线粒体DNA标记位点；euka2引物对（Guardiola等人，2015年）靶向真核生物18S核糖体RNA的V7区域标记位点；bact2引物对（Taberlet等人，2018年）靶向原核生物16S核糖体RNA的V4区域标记位点。本实验设计旨在全面解析群落结构，通过euka2-metazoa-teleo的嵌套层级体系，实现对动物群落（尤其是鱼类）更精细的分类学分辨率。每个样本设置12次PCR重复实验，并同步设置提取空白对照与PCR阴阳对照进行平行分析。仅针对使用teleo引物扩增的PCR重复样本设置唯一标签，以便在后续生物信息学分析中实现样本区分。下一代测序（NGS）文库构建与MiSeq双端测序（2×150 bp）工作在法国勒布尔热迪拉克的DNA Gensee实验室完成。 参考文献 Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). 深海高通量测序：海洋峡谷沉积物中细胞外DNA的宏条形码分析. 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). 城市化梯度下生态多样性的遗传特征. 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). 比较环境DNA宏条形码与水下视觉调查法监测热带礁鱼种群. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140 Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). 环境DNA：用于生物多样性研究与监测. 牛津大学出版社. 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). 基于环境DNA宏条形码技术的水生生物多样性下一代监测. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428
