The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (bact2 data)
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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 bact2 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
本数据集关联以下已发表学术论文：Macé, B.、Mouillot, D.、Dalongeville, A.、Bruno, M.、Deter, J.、Varenne, A.、Gudefin, A.、Boissery, P. 与 Manel, S.（2024）。《生命之树环境DNA（environmental DNA, eDNA）元条形码测序揭示海港与海洋保护区间分类丰富度相似但进化谱系不同》，发表于*Molecular Ecology*，文章编号e17373，DOI: 10.1111/mec.17373。 本数据集包含通过bact2标记（bact2 marker）获取的实验数据： fastq文件为原始下一代测序（Next-Generation Sequencing, NGS）eDNA测序产出文件；dat文件记录测序所用接头名称与寡核苷酸序列。同时提供了每份eDNA样本的关联元数据。 ## 实验方法 eDNA提取在专门用于eDNA样本的生物安全二级（BioSafety Level 2, BSL-2）实验室中完成，严格遵循Polanco Fernández等人（2021）发表的实验流程。本研究共开展4组PCR扩增，采用覆盖全生命之树的不同引物体系： 1. teleo引物对（Valentini等，2016）：靶向硬骨鱼与软骨鱼的12S线粒体DNA标记； 2. 后生动物引物对（Kelly等，2016）：靶向后生动物的16S线粒体DNA标记； 3. euka2引物对（Guardiola等，2015）：靶向真核生物18S核糖体RNA V7区的标记序列； 4. bact2引物对（Taberlet等，2018）：靶向原核生物16S核糖体RNA V4区的标记序列。 本实验设计旨在全面解析群落组成，通过euka2-后生动物-teleo的嵌套层级体系，实现对动物群落（尤其是鱼类）更精细的分类分辨率。每个样本设置12次PCR重复，同步设置提取空白对照、PCR阳性与阴性对照。仅针对使用teleo引物扩增的PCR重复添加唯一标签，以便在后续生物信息学分析中实现样本区分（详见后文）。NGS文库制备与MiSeq双端测序（2×150 bp）在法国勒布尔热-迪拉克（Le Bourget-du-Lac）的DNA Gensee实验室完成。 ## 参考文献 1. Guardiola, M.、Uriz, M. J.、Taberlet, P.、Coissac, E.、Wangensteen, O. S. 与 Turon, X.（2015）。《深海、深度测序：海洋峡谷沉积物中胞外DNA的元条形码分析》，*PLOS ONE*，10(10)，e0139633。DOI: 10.1371/journal.pone.0139633 2. Kelly, R. P.、O’Donnell, J. L.、Lowell, N. C.、Shelton, A. O.、Samhouri, J. F.、Hennessey, S. M.、Feist, B. E. 与 Williams, G. D.（2016）。《沿城市化梯度的生态多样性遗传特征》，*PeerJ*，4，e2444。DOI: 10.7717/peerj.2444 3. 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. 与 Pellissier, L.（2021）。《比较环境DNA元条形码与水下视觉普查以监测热带礁鱼类》，*Environmental DNA*，3(1)，142–156。DOI: 10.1002/edn3.140 4. Taberlet, P.、Bonin, A.、Zinger, L. 与 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。 5. 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. 等（2016）。《利用环境DNA元条形码技术实现水生生物多样性的下一代监测》，*Molecular Ecology*，25(4)，929–942。DOI: 10.1111/mec.13428
