Background: Food-borne nematodes of the genus Anisakis are responsible for a wide</p><p>range of illnesses (= anisakiasis), from self-limiting gastrointestinal forms to severe</p><p>systemic allergic reactions, which are often misdiagnosed and under-reported. In order</p><p>to enhance and refine current diagnostic tools for anisakiasis, knowledge of the whole</p><p>spectrum of parasite molecules acting as potential allergens is necessary.</p><p>Methodology/Principal Findings: In this study, we employ high-throughput (Illumina)</p><p>sequencing and bioinformatics technologies to characterise the transcriptomes of two</p><p>Anisakis species, A. simplex and A. pegreffii, and mine these annotated datasets to</p><p>compile lists of potential allergens from these parasites. A total of ~65,000,000 reads</p><p>were generated from cDNA libraries for each species, and assembled into ~34,000</p><p>transcripts (= Unigenes) ~18,000 peptides were predicted from each cDNA library and</p><p>classified based on homology searches, protein motifs and gene ontology and</p><p>biological pathway mapping. Using comparative analyses with sequence data available</p><p>in public databases, 36 (A. simplex) and 29 (A. pegreffii) putative allergens were</p><p>identified, including sequences encoding 'novel' Anisakis allergenic proteins (i.e.</p><p>cyclophilins and ABA-1 domain containing proteins).</p><p>Conclusions/Significance: This study represents a first step towards providing the</p><p>research community with a curated dataset to use as a molecular resource for future</p><p>investigations of poorly known putative Anisakis allergens, using functional genomics,</p><p>proteomics and immunological tools. Ultimately, an improved knowledge of the</p><p>biological functions of these molecules in the parasite, as well as of their immunogenic</p><p>properties, will assist the development of comprehensive, reliable and robust</p><p>diagnostic tools.