R software environment

For miniature recordings, we used a modified intracellular solution to adjust the reversal potential of the GABA_A receptor response [127.5 mM cesium methanesulfonate, 7.5 mM CsCl, 10 mM HEPES, 2.5 mM MgCl₂, 4 mM Na₂ATP, 0.4 mM Na₃GTP, 10 mM sodium phosphocreatine, 0.6 mM EGTA (pH 7.25)]. Moreover, we added 0.5 µM tetrodotoxin (Wako Pure Chemicals, Osaka, Japan) to perfusate to block action potentials. The voltage was clamped at −60 mV for mEPSC recording and at 0 mV for mIPSC recording (Figs. 2A and 3A). We analyzed the frequency and amplitude of mEPSCs and mIPSCs above 10 pA.
We obtained 4 miniature parameters (mean mEPSC amplitude, mean mIPSC amplitude, mean mEPSC frequency, and mean mIPSC frequency) in individual CA1 pyramidal neurons. For graphic expression, the distribution was visualized 2-dimensionally in the R software environment (R Foundation for Statistical Computing, Vienna, Austria) (amplitude in Fig. 2B; frequency in Fig. 3B). To calculate E/I balance, the value of mEPSC frequency or amplitude was divided by corresponding value of mIPSC frequency or amplitude in each neuron. After recording, we confirmed that mEPSCs and mIPSCs were completely abolished by 10 µM CNQX (MilliporeSigma, Burlington, MA, USA) and 10 µM bicuculline methiodide (MilliporeSigma), respectively.

Plates were scanned at 600 dpi resolution. Primary root length was measured using the NeuronJ plugin in Fiji package (https://fiji.sc; version 1.0). For the eru mutant, primary root images were recorded using a Nikon AZ100 multizoom macroscope and primary root length was measured using ImageJ. Data was analysed and visualised using R software environment (R Foundation for Statistical Computing, Vienna, Austria; https://www.r-project.org; version 3.3.3).

All of the statistical analysis was conducted using the R software environment (R Foundation for Statistical Computing). One-way ANOVA with Scheffe post-testing was used to compare results among different groups. The logistic regression was calculated using the Pearson Chi-square test. Cell proliferation was plotted with the general plot function and ggplot2 with the geom_line function. The gene heatmap was plotted using the heatmap function. The cluster analysis was conducted by using Ward’s hierarchical agglomerative clustering method. Survival data and gene expression values (fragments per kilobase per million mapped fragments, FPKM) were withdrawn from the Human Protein Atlas for use in the Kaplan-Meier plots

Chi‐square tests (χ2) were applied to determine whether F. circinatum caused pre‐emergence mortality equally on the Scots pine populations at the three inoculum doses tested (50, 10³, 10⁶ spore ml⁻¹). Yates' correction for continuity was applied in those cases where the expected frequencies were below 5. Survival analysis based on the Kaplan–Meier nonparametric estimator (Kaplan and Meier, 1958) was carried out with the ‘Survival’ package (Therneau, 2017) to test post‐emergence mortality to the end of the experiment. Survival curves were created with the ‘Survfit’ function and differences between the curves tested with the ‘Survdiff’ function. All analyses were performed using R software environment (R Foundation for Statistical Computing,).