Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i>

Production of the neurotoxin domoic acid (DA) by benthic diatom <i>Nitzschia navis-varingica</i> poses considerable health and economic concerns. In this study, we employed whole genome sequencing and transcriptomic analyses of regionally distinct <i>N. navis-varingica</i> strains to unravel the genomic underpinnings of DA biosynthesis. Our analyses revealed sizable genomes-characterized by an abundance of repetitive elements and noncoding DNA-that exceed the size of any other pennate diatoms. Central to our findings is the discovery of an expanded domoic acid biosynthesis (<i>dab</i>) gene cluster, spanning over 60 kb and marked by a unique organization that includes core genes interspersed with additional genetic elements. Phylogenetic and syntenic comparisons indicate that transposition events may have driven the expansion and reorganization of this cluster. Biochemical assays validated that the kainoid synthase encoded by <i>dabC</i> catalyzes the formation of isodomoic acid B, thereby establishing a distinct chemotype in contrast to the DA profiles of planktonic diatoms. These results highlight the evolutionary trajectory of DA biosynthesis in diatoms and potential advantages conferred by genome expansion and enzyme diversification in dynamic marine environments.IMPORTANCEDomoic acid (DA) is a potent neurotoxin produced by marine micro- and macroalgae problematic to fisheries and toxic to humans and animals. Our study elucidates the molecular mechanisms underlying DA production in the widespread Western Pacific benthic diatom, <i>Nitzschia navis-varingica</i>. Genomic and biochemical insights add information to our understanding of the evolution of toxin production across diverse phyla and also fill a gap in the knowledge of secondary metabolism in marine diatoms. These findings provide a genetic framework for identifying toxin production and its impacts in the benthos of vulnerable, coastal ecosystems.