Data from: High-throughput sequencing of nematode communities from total soil DNA extractions

Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDNA背景：线虫（nematode）类群多样性极高，预估物种总数超百万。采用传统标准方法（如基于形态学的物种鉴定）开展线虫多样性研究，不仅难度颇高且耗时耗力，因此高通量测序成为极具吸引力的替代方案。通常，以往用于制备测序扩增子的引物并非线虫特异性引物，同时还会扩增真菌、植物等其他类群的序列，因此必须增设线虫富集步骤，但该步骤可能引入实验偏差。 结果：本研究开发了一种搭载新型引物的扩增策略，可选择性扩增线虫及其他后生动物（metazoans）的序列。将该策略应用于22份农业土壤的DNA模板进行验证时，最终获得的序列中总计64.4%源自线虫，剩余序列几乎全部属于后生动物。所得线虫序列覆盖了广泛的分类类群，其中多数序列来自此前已被证实为土壤优势类群的线虫类群，包括垫刃目（Tylenchida）、小杆目（Rhabditida）、矛线目（Dorylaimida）、三孔目（Triplonchida）以及色矛目（Araeolaimida）。 结论：本研究开发的这款用于线虫多样性评估的扩增与测序策略，无需预先开展线虫富集即可覆盖广泛的线虫分类类群，因此该方法在线虫生态学研究中具备极高的应用价值。 关键词：线虫、群落、下一代测序、SSU、多样性、18S、核糖体DNA（rDNA）