*3.2. Alternaria and Aspergillus Metabolites*/*Mycotoxins in Fusarium-Inoculated and Naturally-Infected Samples*

Concentrations of six *Alternaria* and *Aspergillus* metabolites/mycotoxins in *Fusarium*-inoculated and naturally-infected samples of four wheat varieties are presented in Figure 2. Alternariol was detected only in variety Mv Karizma, in both inoculated and naturally-infected samples (Figure 2a). The highest concentration of alternariolmethylether was detected in naturally-infected Mv Karizma (6 μg/kg), while naturally-infected Pepeljuga and Ficko in both treatments had no alternariolmethylether (Figure 2b). Altersetin, infectopyron, tentoxin, and tenuazonic acid were detected in all varieties in both treatments

(Figure 2c–f). In naturally-infected samples, compared to inoculated samples, the mean infectopyron and tentoxin concentrations were significantly increased (Supplementary Figure S2, Figure 2a,b). The *Aspergillus* metabolite kojic acid was found only in FHB-inoculated samples of Ficko and Pepeljuga (Figure 2g).

### *3.3. Other Metabolites in Fusarium-Inoculated and Naturally-Infected Samples*

Concentrations of additional five unspecific metabolites in *Fusarium*-inoculated and naturally-infected samples are presented in Figure 3. Brevianamid F was found in both treatments in Ficko, and in naturally-infected samples of Mv Karizma and Mv Kolompos (Figure 3a). Butenolid was found in all samples with increased concentrations in inoculated samples compared to naturally-infected samples (Figure 3b) (Supplementary Figure S2, Figure 2e). Cyclo(L-Pro-L-Tyr) and cyclo(L-Pro-L-Val) were increased in inoculated samples (Figure 3c,d), while tryptophol had higher concentrations in naturally-infected samples (Figure 3e).

**Figure 3.** Other metabolites in *Fusarium*-inoculated and naturally-infected samples: brevianamid F (**a**), butenolid (**b**), cyclo(L-Pro-L-Tyr) (**c**), cyclo(L-Pro-L-Val) (**d**), and tryptophol (**e**). The asterisk (\*) indicates < LOD.

There were no observed statistical differences between different wheat varieties tested by Kruskal–Wallis ANOVA (data not shown).
