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.