engleski

Discovery of genome-wide SNPs by ddRAD sequencing for two ectoparasites, Sparicotyle chrysophrii and Ceratothoa oestroides, that impact Mediterranean finfish culture

Interactions between wild and farmed fish, in the context of parasite transmission between populations, remain poorly understood. Wild fish may be drawn into the vicinity of farms through the presence of abundant food, provision of shelter or by signals from conspecifics and can serve as reservoirs of parasite transmission. Similarly, cultured stocks may act to amplify infectious stages in the environment, as they may be present in high numbers, be more susceptible to disease than wild fish and may accumulate higher parasite burdens due to intense rearing conditions. The monogenean Sparicotyle chrysophrii and the cymothoid isopod Ceratothoa oestroides have been identified as the most devastating ectoparasites in Mediterranean aquaculture, inflicting losses primarily in gilt head sea bream Sparus aurata and European sea bass Dicentrarchus labrax production. Their life cycles and modes of transmission have not been completely elucidated and molecular resources for their investigation are extremely scarce. In order to address this, we have used a genotyping- by-sequencing approach, double digest Restriction-site Associated DNA sequencing (ddRAD-Seq), to generate a genome-wide SNP marker dataset with the long term aim of investigating the degree of differentiation among individuals collected from farmed and wild hosts. Initial trials were conducted with S. chrysophrii and C. oestroides samples collected from Croatian and Greek farms. Two separate ddRAD libraries for S. chrysophrii and C. oestroides were constructed (96 and 138 samples in total), producing over 16 and 21 million reads with 26, 566 and 95, 697 unique RAD loci identified respectively. Considerable variability in number of reads, polymorphic loci and SNPs identified was observed between individuals for both species. SNPs genotyped in at least 50% of the individuals were identified (507 in S. chrysophrii and 1, 364 in C. oestroides) and used to compare the structure between samples currently available: wild and farmed S. chrysophrii and F1 and F2 offspring propagated in the laboratory for C. oestroides. The results provide a baseline for development of new ecological and biological studies of these species, using new genomic tools and resources, with important implications for aquaculture management and practice.

Sparicotyle chrysophrii, Ceratothoa oestroides, ddRAD, SNPs, aquaculture, wild-farmed transmission

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