Development and characterization of novel microsatellite markers in the Manila clam parasitic arthropods, Nymphonella tapetis (Pycnogonida, Ascorhynchidae), using next-generation sequencing

Nymphonella tapetis is a marine parasite that infects bivalves, including the Manila clam, and has caused significant fishery damage in Japan from 2007 to 2009. To detect the genetic diversity and analyze the population structures of this species, this study aimed to isolate microsatellite markers for N. tapetis using next-generation sequencing. A total of 1,095 microsatellite regions were identified, and 36 primer sets were successfully amplified by PCR. Among these, 13 reproducible polymorphic loci were selected for the genetic analysis of N. tapetis individuals from Japan. The primers were specific to N. tapetis and showed high polymorphism, so they were used for population genetics studies. No significant deviation from Hardy-Weinberg equilibrium was observed at all these loci, indicating random mating in the population. No significant difference was observed in allele frequency at these loci was observed among three regional samples (Futtsu and Banzu in Chiba Prefecture, and Mikawa Bay in Aichi Prefecture). These showed that Futtsu, Banzu, and Mikawa Bay populations are genetically similar with one another, suggesting that they originated from the same ancestral population. However, allelic richness in the Futtsu tidal flat population was higher, possibly indicating that it as the source for the other populations. • Isolated microsatellite markers via next-generation sequencing from Nymphonella tapetis. • A thousand ninety-five microsatellite regions were found and developed 36 primer sets. • Thirteen reproducible markers were selected for the analysis of Japanese populations. • Genetic analysis suggested frequent gene flow among the three regions in Japan. • N. tapetis in Japan is considered to have originated from the same ancestral population.