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Microsatellite markers for the dinoflagellate Gambierdiscus caribaeus from high-throughput sequencing data

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Abstract

Members of the benthic dinoflagellate genus Gambierdiscus are the causative agents of ciguatera fish poisoning worldwide. Ciguatera outbreaks appear to be more common in recent years and new incidences are reported from unprecedented regions. To investigate Gambierdicus population dynamics, connectivity, and dispersal routes, we developed microsatellite markers for Gambierdiscus caribaeus, a globally distributed species that is common at our study site at St. Thomas in the US Virgin Islands. We used high-throughput partial genome sequencing along with an existing transcriptome for microsatellite discovery. Screening of contigs with less than three times coverage resulted in 558 (partial genome) and 33 (transcriptome) candidate microsatellites. Four primer pairs from the partial genome and three from the transcriptome successfully amplified polymorphic microsatellites in multiplexed PCR reactions. The seven markers were tested on 150 G. caribaeus strains isolated monthly from August 2013 to July 2015 at St. Thomas, USVI. The numbers of alleles per locus varied between 3 and 14, and the allele diversity ranged from 0.214 to 0.899 in this dataset. These newly developed microsatellites will enable studies of population structure, connectivity, and dispersal in G. caribaeus and can give new insights into the expansion of ciguatera outbreaks worldwide.

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Acknowledgements

We thank Kathleen Pitz and Donald Anderson from Woods Hole Oceanographic Institution for providing the transcriptome of Gambierdiscus caribeaus. Yesid Lozano-Duque greatly contributed to the isolation, cultivation, and DNA extraction of Gambierdiscus strains from St. Thomas. We are grateful for the constructive comments from two anonymous reviewers on this manuscript. This article is a result of research funded by the National Oceanic and Atmospheric Administration Center for Sponsored Coastal Ocean Research ECOHAB program under award no. NA11NOS4780061 to the University of Texas Marine Science Institute (D.L.E.). This is publication #ECOHAB881.

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Correspondence to Ingrid Sassenhagen.

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Sassenhagen, I., Erdner, D.L. Microsatellite markers for the dinoflagellate Gambierdiscus caribaeus from high-throughput sequencing data. J Appl Phycol 29, 1927–1932 (2017). https://doi.org/10.1007/s10811-017-1076-8

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  • DOI: https://doi.org/10.1007/s10811-017-1076-8

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