Domoic acid (DA) is the neurotoxin responsible for amnesic shellfish poisoning long thought to be confined to only two phylogenetically related diatom genera Pseudo-nitzschia and Nitzschia in one class Bacillariaceae, leaving the occurrence and evolutionary origin of this trait in other diatom classes unresolved. Here we revealed widespread homologs of DA biosynthesis (dab) genes across diverse diatom lineages through large-scale mining of Tara Oceans metatranscriptomes, suggesting that the genetic potential for DA production is far more pervasive than previously recognized. We identified dab genes in Chaetoceros costatus (class Mediophyceae) through genome-based screening of 281 diatom strains representing 54 diatom species from Chinese waters. The C. costatus genome encodes three of the canonical dab genes but lacked dabB, which is similarly absent in DA-producing red alga Chondria armata. Analytical validation using LC-MS/MS confirmed DA production in the strains, indicating that dab genes in C. costatus are functionally active. Chromosome-level genome assemblies revealed haplotype-specific expansions of dabA and dabD, suggesting possible key functions in diversifying DA biosynthetic capacity. Phylogenetic analyses revealed multiple horizontal gene transfer events, including at least one cross-eukaryote acquisition between Pseudo-nitzschia and C. costatus. These findings substantially expand the known taxonomic range of DA-producing diatoms and highlight the hidden toxin potential of ecologically dominant marine diatoms.

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