Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

Domoic acid (DA) production by diatom genus Pseudo-nitzschia causes recurrent harmful algal blooms with major consequences for marine ecosystems, fisheries, and human health. Predicting DA risk remains challenging because toxin production varies across morphologically similar and cryptic lineages. Consequently, morphology or single marker genes often fail to resolve toxigenic potential. Here, we expand genomic resources for Pseudo-nitzschia by generating and compiling high-quality genomes spanning diverse species and biogeographic origins, establishing a genus-wide phylogenomic framework to investigate the distribution and evolution of the DA biosynthesis (dab) gene cluster. Among chemically characterized strains, the dab pathway was detected in species only with confirmed DA production. While the cluster exhibits a conserved core structure, several lineages display signatures of ongoing evolution, including intronization, locus rearrangement, and pseudogenization. One striking example of dab variation occurs in toxigenic P. australis strains, in which its biochemically validated isodomoic acid A synthase-encoding gene dabC is located outside the dab locus. Metatranscriptomic surveys reveal widespread environmental dab expression across size classes and species, implicating taxa not typically associated with environmental DA events, such as P. cf. obtusa and P. cf. plurisecta. To connect dab expression with chemical output, nutrient limitation experiments in the historically inconsistent DA producer P. pseudodelicatissima combined transcriptional profiling and nontargeted metabolomics demonstrating coordinated dab expression across distinct co-expression modules and DA accumulation in response to silicon limitation. Together, these results refine the phylogenetic scope of DA production and provide a genome-resolved basis for improved molecular monitoring of toxigenic diversity.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-10-27
DOI
https://doi.org/10.64898/2026.10.23.761457
Primary Topic
Marine Toxins and Detection Methods
Type
preprint
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preprint

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

Zoltán Füssy, Freya Hammar, Andrés Mauricio Caraballo‐Rodríguez, Steffaney Wood et al.
bioRxiv (Cold Spring Harbor Laboratory)
Marine Toxins and Detection Methods
preprint

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

Zoltán Füssy, Freya Hammar, Andrés Mauricio Caraballo‐Rodríguez, Steffaney Wood, Tom O. Delmont, Shelly A. Wanamaker, Bradley S. Moore, Matthew J. Harke, Monica Thukral, Andrew Ellis Allen, Nathalie Choisne, Katherine A. Hubbard, Brian D. Bill, Jennifer M. Polinski, Pieter C. Dorrestein, Florian Maumus, Hong Zheng, Alexandra DeSmidt, Hannah McGrath
preprint en

Abstract

Domoic acid (DA) production by diatom genus Pseudo-nitzschia causes recurrent harmful algal blooms with major consequences for marine ecosystems, fisheries, and human health. Predicting DA risk remains challenging because toxin production varies across morphologically similar and cryptic lineages. Consequently, morphology or single marker genes often fail to resolve toxigenic potential. Here, we expand genomic resources for Pseudo-nitzschia by generating and compiling high-quality genomes spanning diverse species and biogeographic origins, establishing a genus-wide phylogenomic framework to investigate the distribution and evolution of the DA biosynthesis (dab) gene cluster. Among chemically characterized strains, the dab pathway was detected in species only with confirmed DA production. While the cluster exhibits a conserved core structure, several lineages display signatures of ongoing evolution, including intronization, locus rearrangement, and pseudogenization. One striking example of dab variation occurs in toxigenic P. australis strains, in which its biochemically validated isodomoic acid A synthase-encoding gene dabC is located outside the dab locus. Metatranscriptomic surveys reveal widespread environmental dab expression across size classes and species, implicating taxa not typically associated with environmental DA events, such as P. cf. obtusa and P. cf. plurisecta. To connect dab expression with chemical output, nutrient limitation experiments in the historically inconsistent DA producer P. pseudodelicatissima combined transcriptional profiling and nontargeted metabolomics demonstrating coordinated dab expression across distinct co-expression modules and DA accumulation in response to silicon limitation. Together, these results refine the phylogenetic scope of DA production and provide a genome-resolved basis for improved molecular monitoring of toxigenic diversity.

bioRxiv (Cold Spring Harbor Laboratory)
Centre National de la Recherche Scientifique (FR), J. Craig Venter Institute (US), National Oceanic and Atmospheric Administration (US), Scripps Institution of Oceanography (US), Florida Fish and Wildlife Conservation Commission (US), University of Washington (US), AgroParisTech (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), University of California San Diego (US), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Génomique Métabolique du Genoscope (FR), Institut Jean-Pierre Bourgin (FR), Genoscope (FR), Gloucester Marine Genomics Institute (US), NOAA National Marine Fisheries Service Northwest Fisheries Science Center (US), Moss Landing Marine Laboratories (US)
Marine Toxins and Detection Methods
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