**2. Materials and Methods**

### *2.1. Plant Lines and Fungal Strains*

Bioassays were performed either on the tomato (*Solanum lycopersicum*) line C32 or Money Maker, susceptible to *Fusarium* wilt, or on the wild tomato relatives *S. pimpinellifolium* (accession LA1578) and *S. chmielewskii* (accessions LA1840, LA2663 and LA2695) in a climate-controlled greenhouse with a day-night temperature of 25◦C, 16 h light/ 8 h dark, and a relative humidity of 65%. Fol029 (race 3, sFP2381, carrying phleomycin resistance [18]) and Fo47 (sFP1544, carrying hygromycin resistance, [19]) were inoculated on the aforementioned tomato lines. Bioassays using various *Fusarium* species were performed on the tomato line C32 using the wild-type pathogen Fol4287 (sFP801) [20], and endophyte Fo47 (sFP730) [10], *F. hostae* (sFP2236), *F. proliferatum* (sFP2240), *F. redolens* (sFP4856) [21], and *F. solani* (sFP895). To facilitate fungal reisolation from tomato stems transgenic fungi caring di fferent resistance markers were used. Therefore, the endophytic strain Fo47 containing hygromycin resistance (sFP1544) and the pathogenic strain Fol4287 (race2, SFP3858) [22] or Fol029 (race 3, sFP2381) were used for the reisolation experiments. Strains used in bioassays are described in the supplementary material are the following: Fo47 (sFP1544, [19]), Fol4287 (sFP3059, [23]), Fo47 (sFP730), Fol4287 (sFP801), and Fol017 (sFP17, [24]).

### *2.2. Fusarium Inoculation and Disease Scoring*

*Fusarium* strains were grown on potato dextrose agar (PDA) plates for seven to ten days at 25◦C in the dark. An agar plug from these plates was transferred to 100 mL of NO3 minimal media (1% KNO3, 0.17% Yeast Nitrogen Base without amino acids and ammonia and 3% sucrose) and incubated at 150 rpm for 3-5 days at 25◦C. Spores were filtered over one layer of miracloth filter (Millipore), centrifuged at 2000 rpm, washed with sterile water, and finally resuspended in sterile MiliQ-water. Ten-day-old or 13-days-old tomato seedlings were uprooted, and their roots were trimmed to facilitate *Fusarium* infection. Subsequently, tomato roots were dipped for five minutes in a suspension of 107 spores/mL or 107 spores/mL: 107 spores/mL (ratio 1:1) in the case of the coinoculation treatments if not stated di fferently. After inoculation, the seedlings were potted, and three weeks afterwards fresh weight and disease index were assessed as described [9]. In short, the disease score was based on the number of brown vessels and external growth wilting symptoms, where 0= healthy plant with no brown vessels; 1= brown vessel(s) only at the basal level; 2= one or two brown vessels at the cotyledon level, the plant still looks healthy; 3= at least three brown vessels and the plant shows clear external witling symptoms; 4= all vessels are brown and the plant shows clear size reduction; and 5= plant is dead. Fresh weight was measured by determining weight of each tomato plant cut at cotyledon level.
