Outbreaks of paralytic shellfish poisoning caused by the toxic dinoflagellate Alexandrium catenella (Dinophyceae) are currently a serious global problem both from economic and food hygiene perspectives. In Chile, A. catenella was first recorded in 1972 and is currently the main harmful algae species in the country, in terms of seafood security. As no relevant microsatellite markers for Chilean A. catenella populations were available, we isolated 23 new polymorphic microsatellite loci of A. catenella from Chile, of which 15 are applicable to both Chilean and Japanese populations. We found a strong genetic break between Chilean and Japanese A. catenella populations (F ST =0.298, P<0.001), consistent with the morphological differences between them. In contrast to the Japanese population, for which genetic diversity ranged from 0.268 to 0.937, the Chilean population had a lower genetic diversity, ranging between 0.065 and 0.512. This study successfully developed A. catenella microsatellite markers that can be used to investigate its genetic spatial and temporal bloom diversity and assess further genetic connectivity between the population from southern and northern Chilean areas.
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