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To better understand the molecular mechanisms underlying allergens and parasite immunity and discover the stage-enriched gene expression of fish-borne zoonotic nematodes in the stomach, we used RNA-seq to study the transcriptome profiles of Anisakis pegreffii (Nematoda Anisakidae, AP) in simulated gastric juice. Mobile L3 larvae were incubated in simulated medium at 37 °C in 5% CO2 (AP-GJ) and the control group larvae were collected in PBS under the same conditions (AP-PBS). We found that the sequences of A. pegreffii were highly simila