Data from: A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing

Molecular analysis of predator gut content is a popular tool to uncover food web structure and has greatly profited from the emergence of next-generation sequencing technology. However, the molecular recovery of prey spectra comes with many challenges, particularly the overabundance of predator DNA in extractions. When predator and prey are distantly related, predator-specific blocking primers can be used to preferentially amplify prey DNA. But this is difficult in the case of arthropods, where prey and predator are often closely related. Here, we present a simple and cost-efficient protocol for high-throughput analysis of the gut content of predatory arthropods without the need for blocking primers. We test several factors for their potential to enrich prey DNA from extractions of predators, including size selection of DNA, selection of different body parts for extraction, and variation in extraction lysis time and PCR fragment length. Using a locally abundant spider species (Hololena adnexa, Agelenidae), we show that prey DNA can be significantly enriched from predator extracts by selectively removing high molecular weight DNA and by extracting from the midgut and hindgut only. A comparison of our results with observational data from other agelenid spider species indicates a high efficiency of our approach. Our enrichment protocol allows for the parallel analysis of several hundred predators in a single MiSeq run, reducing the cost per specimen to only a few dollars and requiring a simple and minimal work flow. This will enable large-scale and ecosystem-wide analyses of niche differentiation and food web structure.捕食者肠道内容物的分子分析是揭示食物网结构的常用研究手段，且得益于下一代测序（next-generation sequencing）技术的问世而实现了快速发展。然而，通过分子手段获取猎物谱系仍面临诸多挑战，其中尤以提取物中捕食者DNA过量的问题最为显著。当捕食者与猎物亲缘关系较远时，可使用捕食者特异性阻断引物（blocking primers）优先扩增猎物DNA。但在节肢动物（arthropods）类群中，该方法难以实施，因为其捕食者与猎物往往亲缘关系密切。 本研究提出一种无需阻断引物即可实现捕食性节肢动物肠道内容物高通量分析的简便且经济高效的实验方案。我们测试了多种可从捕食者提取物中富集猎物DNA的潜在影响因素，包括DNA片段大小筛选、用于提取的不同躯体部位选择、提取裂解时长以及PCR扩增片段长度的差异。 本研究以本地优势蜘蛛物种Hololena adnexa（漏斗蛛科Agelenidae）为实验材料，证实通过选择性去除高分子量DNA，且仅从中肠和后肠进行提取，可显著富集捕食者提取物中的猎物DNA。将本研究结果与其他漏斗蛛科蜘蛛物种的观测数据进行对比后可知，本方法具备极高的应用效率。 该富集方案可在单次MiSeq测序运行中并行分析数百个捕食者样本，将单个样本的检测成本降至仅数美元，且仅需简单极简的实验流程。这将为生态系统尺度下的生态位分化与食物网结构开展大规模分析提供有力支撑。