The Japanese fire-bellied newt Cynops pyrrhogaster, endemic to mainland Japan is ranked as Near Threatened in the red list of Japan. However, microsatellite markers effective for estimating genetic diversity and structures for its conservation measures have never been reported. Therefore, we developed fifteen novel microsatellite markers for this species using expressed sequence tag and next-generation sequencing data. The number of alleles and expected heterozygosity at each locus were 3-28 (mean = 11.6) and 0-0.97. The markers described here will be useful for investigating the genetic diversity and genetic structure, and planning conservation management of C. pyrrhogaster.
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