Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling.

•A RNA-seq approach was used to study the global and without a priori response of oyster to the toxic Alexandrium minutum.•Toxin load was the main driver of transcriptomic variations.•A limited number of metabolic pathways in oysters covaried with PST load.•A correlation between PST load and transcript abundance described by only 70 of the ∼29,000 oyster genes was shown.•Association between toxin load, genotype, and mRNA level opens new doors to investigate PST inter-individual variability.