SSR marker development for Japanagromyza tokunagai (Agromyzidae, Diptera) using genome sequences obtained by nanopore sequencing.

Japanagromyza tokunagai Sasakawa 1953 (Agromyzidae, Diptera) disrupts seed reproduction of orchids by feeding on orchid fruit. This species has been feeding on orchid fruits in Japan for more than 100 years, but the recent increase in damage may be due to the spread of particularly harmful populations. In this study, we used nanopore sequencing to establish microsatellite markers for J. tokunagai to infer the cause of this fly's spreading history based on population genetic analysis of historical specimen origin and current samples. Analysis of three populations showed that all 15 loci of microsatellite markers established were polymorphic and the number of alleles ranged between 3 and 13. The markers developed in this study can be used to reveal current and past population genetic diversity and gene flow, contributing to our understanding of the population history of this parasitic fly. Further research using these markers will provide a foundation for the developing control methods for J. tokunagai and support the conservation of rare orchid plants.