Syngnathids (pipefishes, seahorses and seadragons) are vulnerable to human-mediated habitat perturbation. The Pacific seaweed pipefish Syngnathus schlegeli has a large distribution in the northwestern Pacific, where deterioration, loss and fragmentation of its seagrass habitat are occurring through coastal development. So far, few studies have been conducted to access the genetic structure and conservation status of S. schlegeli because of the low number of genetic markers currently described. Nineteen polymorphic microsatellite markers were developed for S. schlegeli using next-generation sequencing, and characterized in 32 individuals. The mean number of alleles was 14, with 2-28 alleles per locus. The estimates of observed heterozygosity (H) and expected heterozygosity (H) varied depending on the locus, ranging from 0.063 to 1.000, and from 0.062 to 0.969, respectively. Seventeen of the 19 microsatellites conformed to Hardy-Weinberg equilibrium. These new microsatellite markers should provide a wealth of information for studies on conservation genetics and the behavioral ecology of S. schlegeli.
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