Application Of High-Throughput Sequencing (Hts) Metabarcoding To Diatom Biomonitoring: Do Dna Extraction Methods Matter?

The 8 benthic samples from Mainland France (stream Edian, stream Aire, lake Geneva), Sweden (stream Dåmman, Agricultural stream, lake Båtkåjaure) and Mayotte (stream Dapani, stream Majimbini) were collected by scraping material from the surface of stones, following the French standard (AFNOR 2007) used in routine biomonitoring programs.DNA was extracted from each sample (2 replicates) using five DNA extraction methods, followed by the amplification of a short rbcL DNA barcode (312bp) specific to diatoms. PCR products were then sequenced in one random direction using the Ion Torrent™ Personal Genome Machine® (PGM) System according to the manufacturer’s instructions. The data file contains one fastq file per library sequenced with the raw DNA reads, as provided by the sequencing platform (demultiplexing performed by the sequencing platform). An excel file is also provided to make the link between the fastq file number and the sample information (sample origin, DNA extraction method used, number of raw reads).采自法国本土（埃迪安河、艾尔河、日内瓦湖）、瑞典（达曼河、农业溪流、巴特科约雷湖）以及马约特岛（达帕尼河、马津比尼河）的8份底栖样本，通过刮取石块表面物质获取，采集流程遵循常规生物监测项目所用的法国标准（AFNOR 2007）。对每份样本设置2个生物学重复，采用5种DNA提取方法完成DNA提取，随后扩增针对硅藻的短rbcL DNA条形码（312bp）。随后按照制造商操作指南，使用Ion Torrent™ 个人基因组测序仪（PGM System）对PCR产物进行单端随机测序。本数据集包含测序平台产出的每份测序文库对应的原始DNA读段fastq文件（测序平台已完成样本拆分（demultiplexing））。此外还提供了一份Excel文件，用于关联fastq文件编号与样本信息，包括样本来源、所用DNA提取方法以及原始读段数量。