Environmental DNA Marine France LaPerouse 2019

Fish environmental DNA data set collected in the shallow seamount of La Pérouse located between Madagascar and Réunion Island
In 2019, we sampled the shallow seamount of La Pérouse, located between Madagascar and Réunion Island in the WIO. La Pérouse is an extinct volcano with a summit depth at 60 m below the sea surface. The plateau of the summit has a maximum length of 12 km and a maximum width of 4 km. One side of the seamount might have collapsed in the past, leading to a less common crescent-shaped summit. The abyssal plains that surround this isolated pinnacle are at a depth of 5000 m. Despite its proximity to Réunion Island (160 km northwest), La Pérouse and its surroundings are still poorly studied.
To sample eDNA in this location we used a submersible pump (Subspace, Geneva, Switzerland; nominal flow of ~ 1.0 L/min) to collect samples at various depths during close circuit rebreather dives. The pump has an internal battery and can be activated underwater allowing in situ filtration directly at the targeted habitat and depth. The filtration lasted for 30 min to collect a total water volume of ~ 30 L. During close circuit rebreather dives, water samples from various depths, ranging from 60 to 140 m below the sea surface, were collected using only the Submersible method (eight stations: no replicates). Out of the eight water samples, six were collected during the day, while two were collected at night (IS2_1 at 62 m and IS7_1 at 100–125 m). We applied this filtration protocols to collect and filter water throughout a VigiDNA® 0.2 μM cross-flow filtration capsule (SPYGEN, le Bourget du Lac, France) using disposable sterile tubing for each filtration capsule. After the filtration process, the remaining water in the capsules was emptied. The capsules were then filled with 80 ml of lysis conservation buffer (CL1 buffer SPYGEN, le Bourget du Lac, France) and stored at room temperature in the dark. At La Pérouse, a total of eight water samples were collected during the MONT LA PÉROUSE expedition (https://gombessa-expeditions.com/mont-la-perouse/) on board the ship La Curieuse to the seamount La Pérouse from October 27th to November 5th 2019. We followed a strict contamination control protocol in both field and laboratory stages. Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris).
Data content:
* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

马达加斯加与留尼汪岛之间拉佩鲁兹浅海山鱼类环境DNA数据集

2019年，我们在西印度洋（Western Indian Ocean, WIO）马达加斯加与留尼汪岛之间的拉佩鲁兹浅海山开展采样。拉佩鲁兹为一座死火山，其峰顶深度位于海面以下60米处；峰顶平台最长12千米，最宽4千米。该海山的一侧可能曾发生坍塌，形成了较为罕见的新月形峰顶。环绕这座孤立海峰的深海平原深度达5000米。尽管距留尼汪岛（西北方向160千米）较近，拉佩鲁兹及其周边区域的研究仍十分有限。

为在该区域采集环境DNA（environmental DNA, eDNA）样本，我们在闭式循环呼吸器潜水期间，使用潜水泵（Subspace公司，瑞士日内瓦；额定流量约1.0升/分钟）于不同深度采集样本。该泵内置电池，可在水下启动，从而实现目标生境与深度的原位过滤。过滤持续30分钟，累计采集水量约30升。在闭式循环呼吸器潜水过程中，仅采用潜水泵法于海面以下60至140米的不同深度采集水样（共8个站位，无重复）；其中6个样本于日间采集，2个于夜间采集（IS2_1站位62米处、IS7_1站位100–125米处）。我们采用该过滤方案，通过VigiDNA® 0.2 μM错流过滤胶囊（SPYGEN公司，法国勒布尔热湖）采集并过滤水样，每个胶囊均使用一次性无菌管路。过滤完成后，排空胶囊内残留水分，随即注入80毫升裂解保存缓冲液（CL1缓冲液，SPYGEN公司，法国勒布尔热湖），并于室温避光保存。2019年10月27日至11月5日，我们乘坐‘拉居里厄斯号’（La Curieuse）科考船，在‘蒙拉佩鲁兹’（MONT LA PÉROUSE）考察（https://gombessa-expeditions.com/mont-la-perouse/）期间于拉佩鲁兹海山共采集8份水样。我们在野外与实验室阶段均遵循严格的污染控制协议：每份水样处理均使用一次性手套及单次过滤设备，以规避污染风险。文库制备采用连接法，遵循MetaFast协议（Fasteris公司）。

数据内容：
* rawdata/：包含各样本的原始测序读段（reads）。一个归档文件包含以_R1或_R2后缀标识的双端读段，以及带独立标签的PCR重复样本（若有）；另一个归档文件包含该文库所有提取空白与PCR空白样本。读段已通过cutadapt进行解复用，但未修剪，序列中仍保留独立解复用标签与引物。
* taxadata/：包含生物信息学处理后各样本的所有检测分类单元表（详见Polanco等，2020；https://doi.org/10.1002/edn3.140）及相关野外元数据。
* metadata/：包含两个元数据文件，其一与各过滤器的野外采集数据相关，其二与实验室测序过程相关（含各样本的标签序列、文库名称及标记信息）