Mediterranean-wide SNPs of two aquaculture-important ectoparasites, Sparicotyle chrysophrii and Ceratothoa oestroides, developed by ddRAD sequencing

Abstract

Parasite transmission between wild and farmed fish is poorly understood and controversial, although it has important implications for the reliable and sustainable use of aquatic resources. Wild fish are usually attracted by signals from conspecifics, the food and shelter availability in the farms, and general understanding is that they act as reservoirs for parasite transmission. In addition, cultured stocks may also act as reservoirs of infectious stages in the environment, as they are present in concentrated numbers and density, and potentially more susceptible to disease than wild fish. The monogenean Sparicotyle chrysophrii and the cymothoid isopod Ceratothoa oestroides are recognised as the most devastating ectoparasites in Mediterranean aquaculture, causing losses in gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax) production. Their life cycles and modes of transmission for both ectoparasites have not been fully elucidated and molecular resources for their investigation are extremely scarce. In order to analyse the potential extent of transmission of these two ectoparasites between wild and farmed fish populations, we have used a genotyping-bysequencing approach, double digest Restriction-site Associated DNA sequencing (ddRAD-Seq), to generate a genome-wide SNP marker dataset. Parasites sampling was done across four large Mediterranean farming areas in Spain, Italy, Croatia and Greece, representing the largest collection of genotypes obtained from aquaculture and wild fish populations. Expectedly, we observed a considerable variability in number of reads, polymorphic loci and SNPs between individuals for both species. The results provide a baseline for the development of new ecological and biological studies of these species, using new genomic tools and resources.