Fig. 3

Differentially expressed genes (mRNAs and microRNAs) during nitrogen and phosphate starvation in Amphidinium gibbosum. a Schematic cellular overview of the main differentially expressed genes during nitrogen and phosphate starvation. Orange and blue coloring indicate up- and downregulation, respectively. Green ovals represent plastids, and red boxes indicate mitochondria. A detailed description of proteins is given in Additional file 2: Supplementary Table 9. b Expression profile of PKS and NRPS genes (q < 0.05 and |log2(FC)| > 2) under nitrogen and phosphate starvation. Values show fold changes while N1, N2, and N3; P1, P2, and P3; and NC1, NC2, and NC3 denote triplicate nitrogen, phosphate, and control samples, respectively. Details of the genes are provided in Additional file 2: Supplementary Table 10. NRPS and PKS genes are denoted in red and black, respectively, along the y-axis. c The presence of Dicer (DCL), HEN1, and AGO proteins indicates functional RNAi machinery in A. gibbosum, supported by genomic and transcriptomic data. Whether mature miRNAs in A. gibbosum are methylated is unknown (shaded gray). d Enrichment of miRNA targets during nitrogen starvation shows lactate metabolism as an enriched target process. e The miRNA, agi-miR7721-5p, targets pyruvate metabolism under nitrogen starvation, affecting secondary metabolite biosynthesis. Orange coloring indicates upregulation