Abstract
Freshwater dinoflagellates are typically considered non-toxic, and their polyketides and toxin biosynthesis genes are largely unexplored. Here, we generated and analyzed the transcriptome of freshwater dinoflagellate Palatinus apiculatus and compared it with the transcriptome data from Peridinium bipes and Ceratium furcoides to investigate the presence and diversity of polyketide synthases (PKS), fatty acid synthases (FAS), and saxitoxin (STX) biosynthesis genes (sxt). We identified 95, 117, and 39 PKS-related transcripts in P. apiculatus, P. bipes, and C. furcoides, respectively, which include single-domain PKS, multi-domain PKS, and hybrid NRPS/PKS. Phylogenetic analysis revealed a novel clade of ketosynthase (KS) domains unique to freshwater dinoflagellates, suggesting species-specific diversification. Conserved catalytic residues were found in type II FAS genes across both freshwater and marine taxa. Although core STX biosynthesis genes were absent in all analyzed species, several STX-associated transcripts, including sxtA4, sxtU, sxtS, sxtD, sxtH/T, and sxtI, were identified. Phylogenetic analysis of the sxtA4 domain revealed that freshwater dinoflagellate sequences form a distinct clade from those of toxic marine dinoflagellates and cyanobacteria while retaining conserved active sites, suggesting potential functional variation. These findings reveal unique PKS and STX gene features in freshwater dinoflagellates, highlighting their previously unrecognized biosynthetic diversity, ecological roles, and biotechnological potential.
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Data availability
The datasets generated and/or analysed during the current study are available in the NCBI Sequence Read Archive (SRA) under Bio Project, PRJNA1307768.
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Acknowledgements
We thank Mr. T Kim for cell culture and valuable comments to the early version of our manuscript.
Funding
This work was supported by Korea Environment Industry & Technology Institute (KEITI) through Aquatic Ecosystem Conservation Research Program funded by Korea Ministry of Environment (MOE) (2022003050002 or RS-2022-KE002119211530) and by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (RS-2024-00354842).
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B.L.M designed the research, analyzed the data, wrote the original draft, and reviewed and edited the paper. H.S.K performed the experiment, reviewed and edited the paper. Q.T.N.B. reviewed and edited the paper. J.S.K. designed the research, supervised the research, coordinated with co-authors, and provided extensive feedback on the text.
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Muhammad, B.L., Bui, Q.T.N., Kim, HS. et al. Transcriptomic insights into polyketides and toxin biosynthesis genes in freshwater dinoflagellates. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40315-x
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DOI: https://doi.org/10.1038/s41598-026-40315-x
