Paralytic shellfish toxins (PSTs) are produced by certain species of cyanobacteria and dinoflagellates. Part of the PST biosynthetic pathway has been elucidated in cyanobacteria, and the implication of some sxt genes has been confirmed by experimental studies. Contrary to cyanobacteria, knowledge about PST biosynthesis in dinoflagellates is more limited and generally restricted to comparative studies with the cyanobacterial pathway. To investigate the specificity of the PST pathway in dinoflagellates, 16 toxigenic and nontoxigenic Alexandrium minutum strains from a recombinant cross were compared, without prior assumption about genes or metabolites involved in PST synthesis, using an integrative approach combining untargeted metabolomic and transcriptomic data. Among the 60 most distinguishing transcripts between toxigenic and non‐toxigenic strains, only three sxt genes were present: sxt A4, sxt G, and sxt I. In contrast, non‐ sxt homologs were detected as highly discriminant between these two phenotypes. More specifically, a phy H homolog may act as the analog of the sxt S gene observed in cyanobacteria. Moreover, we identified four putative synthetic PST intermediates. Among these, Int‐C'2 correlated with the toxic phenotype, whereas three others were detected in both toxigenic and nontoxigenic strains, suggesting that these strains may share some parts of the biosynthetic pathway. Finally, our analyses identified both horizontally gained sxt genes and endogenous genes, including the candidate gene phy H, as candidate components of the PST biosynthetic pathway in A. minutum .
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