Genome assembly and SNP resources of Anisakis simplex enable cost-effective population assessment and discrimination...

Anisakis spp are parasitic nematodes that can infect fish during larval stages, and, if consumed by humans, can cause anisakiasis and severe allergic reactions, including anaphylaxis. Here, we generated a 168 Mb genome assembly of A. simplex, the most abundant species in the Northeast Atlantic, which was used to develop SNP resources using a whole genome pooling resequencing strategy. 1,824,098 SNPs and 151,767 short structural variants were identified, showing the high polymorphism and complexity of A. simplex genome. A 481 SNP panel was developed for population screening using the Agriseq technology, through strict filtering and homogeneous distribution across the genome. This panel was used for genotyping 823 larvae and adults of A. simplex, 775 A. pegreffii and 402 putative hybrids collected from different hosts across the Northeast Atlantic, 275 SNPs being consistently genotyped in both species. Among them, 10 SNPs showing extreme genetic differentiation between A. simplex and A. pegreffii and no linkage disequilibrium in A. simplex, were used to design a cost-effective SNP tool for species and hybrid identification in population surveys. The genomic resources obtained will facilitate efficient surveillance programs, accurate discrimination of species and hybrids, effective anisakiasis management in fisheries, and improved seafood safety.