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The dinoflagellate  Karenia mikimotoi  forms blooms in the coastal waters of temperate regions and occasionally causes massive fish and invertebrate mortality. This study aimed to elucidate the toxic effect of  K .  mikimotoi  on marine organisms by using the genomics approach; RNA-sequence libraries were constructed, and data were analyzed to identify toxin-related genes. Next-generation sequencing produced 153,406 transcript contigs from the axenic culture of  K .  mikimotoi . BLASTX analysis against all assembled contigs revealed that 208 contigs were polyketide synthase (PKS) sequences. Thus,  K .  mikimotoi  was thought to have several genes encoding PKS metabolites and to likely produce toxin-like polyketide molecules. Of all the sequences, approximately 30 encoded eight PKS genes, which were remarkably similar to those of  Karenia brevis . Our phylogenetic analyses showed that these genes belonged to a new group of PKS type-I genes. Phylogenetic and active domain analyses showed that the amino acid sequence of four among eight  Karenia  PKS genes was not similar to any of the reported PKS genes. These PKS genes might possibly be associated with the synthesis of polyketide toxins produced by  Karenia  species. Further, a homology search revealed 10 contigs that were similar to a toxin gene responsible for the synthesis of saxitoxin ( sxtA ) in the toxic dinoflagellate  Alexandrium fundyense . These contigs encoded A1–A3 domains of  sxtA  genes. Thus, this study identified some transcripts in  K .  mikimotoi  that might be associated with several putative toxin-related genes. The findings of this study might help understand the mechanism of toxicity of  K .  mikimotoi  and other dinoflagellates.

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi