Data from: Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing

Next generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States’ estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator's diet is essential for a comprehensive understanding of its impact on the food web and its management. Here we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS “shotgun” approach to randomly sequence DNA fragments isolated from gut lavages and gastric pouch/tentacle picks of 8 and 84 sea nettles, respectively. These results were verified by visual identification and co-occurring plankton tows. Over 550,000 contigs were assembled from ~110 million paired-end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves, and hemichordates. Our results not only indicate that a “shotgun” NGS approach can supplement visual identification methods, but targeted enrichment of a specific amplicon/gene is not a prerequisite for identifying Atlantic sea nettle prey items.

下一代测序（NGS）技术已被证实可用于解析广食性捕食者的食物组成，但目前尚未应用于凝胶状动物的肠道及触手内容物分析。NGS技术可作为传统目视鉴定方法的有效补充。大西洋海荨麻（Chrysaora quinquecirrha, Atlantic sea nettle）在美国中大西洋沿岸河口（包括新泽西州巴内加特湾）的种群数量逐渐增多，可能对海洋生物及人类产业造成不利影响。全面解析该捕食者的食性组成，对于深入理解其对食物网的影响并开展针对性管理工作至关重要。本研究旨在验证NGS技术用于大西洋海荨麻捕食对象鉴定的有效性。我们采用NGS“鸟枪法”策略，对分别取自8只海荨麻的肠道灌洗液以及84只海荨麻的胃囊/触手样本中提取的DNA片段进行随机测序。上述测序结果通过目视鉴定以及同期采集的浮游生物拖网样本进行了验证。本研究从约1.1亿条双端读长序列中组装得到超过55万个重叠群（contigs）。其中100个重叠群可明确归类至23个不同的分类单元，涵盖此前未被记录为该捕食者猎物的软体生物，具体包括桡足类、鱼类、栉水母类、海葵类、端足类、蔓足类、虾类、多毛类蠕虫、吸虫类、扁形动物类、棘皮动物类、腹足类、双壳类以及半索动物类。本研究结果表明，NGS鸟枪法不仅可作为目视鉴定方法的有效补充，且无需针对特定扩增子/基因进行靶向富集即可完成大西洋海荨麻的猎物物种鉴定。