Transcriptome responses of the dinoflagellate Karenia mikimotoi driven by nitrogen deficiency

•Transcriptomic analysis revealed 8802 unigenes (3.56%) in K. mikimotoi that responded to nitrogen deficiency.•Under N deficiency, K. mikimotoi shifted to assimilate organic N resource, and cellular N utilization changed to be economical to save N resource.•N limitation increased cellular N recycling via protein degradation and turnover.•K. mikimotoi induced substrate production for triacylglycerol biosynthesis by N starvation.