Fig. 2.

Volcano plots and Venn diagrams showing differentially expressed genes (DEGs) between P starvation and replenishment and their respective controls, at different time points. A-D, volcano plots of 2-day (NP2 vs YP2), 3-day (NP3 vs YP3), 4-day (NP4 vs YP4) and 5-day (NP5 vs YP5) P starvation. E, volcano plot of one-day P replenishment (RP5 vs NP5). A-E, red, green, orange and black indicate the position in the volcano plot, which itself indicates whether they pass or not the significance thresholds: P <  = 0.05 and log2FC >  = 1. Black indicates genes that did not pass any of the thresholds. Orange indicates genes that only pass the log2FC threshold. Red indicates genes that only pass the P threshold. Green indicates genes that pass both thresholds. Blue indicates genes containing plantiSMASH-predicted ‘biosynthetic’ domain [30]. Wine/purple genes belong to plantiSMASH-predicted biosynthetic gene clusters [30]. F-G, Venn diagrams of up- and downregulated DEGs, respectively, at different time points of P deficiency and down- and upregulated, respectively, by P replenishment. PS2_up, PS3_up, PS4_up and PS5_up represent upregulated genes of comparison NP2 vs YP2, NP3 vs YP3, NP4 vs YP4 and NP5 vs YP5, respectively. RP5_down represents the downregulated DEGs by P replenishment (RP5 vs NP5); PS2_down, PS3_down, PS4_down and PS5_down represent downregulated genes of comparison NP2 vs YP2, NP3 vs YP3, NP4 vs YP4 and NP5 vs YP5, respectively; RP5_up represents the upregulated DEGs by P replenishment (RP5 vs NP5)