g. Phaeomoniella chlamydospora, Aureobasidium pullulans, Truncatella angustata, Botrytis cinerea or Phaeoacremonium viticola). Other species, especially closely related species within a single genus (e.g. Cladosporium, Phoma, Alternaria or the anamorphs

of Botryosphaeriaceae and Nectriaceae), JPH203 as well as some species exhibiting a variable morphology on Petri dishes (e.g. Epicoccum nigrum), could not be delimitated based on their vegetative morphology. We first amplified and sequenced the ITS region of a few fungal isolates for all morphotypes. For more plastic morphotypes, we sequenced more isolates. When the sequences obtained for the different isolates of plastic morphotypes were identical, we did not sequence the rest of the isolates grouped in this morphotype. When the sequences of the different isolates of a given morphotype were different we adopted two strategies depending on their similarity BLAST top score in GenBank: either the top score indicated that the isolates belong to the same species and we did not sequence the other isolates, or the BLAST top score indicated that they belonged to different species and we sequenced the ITS region for all isolates, except in the case of Alternaria for which we recovered ITS rDNA genotypes for 216 out of the 523 strains isolated (Online Resource 2) that differed only in the length of a T-repeat at the

end of the ITS2 (see the Discussion section). Having sequenced 907 out of a total of 2595 fungal isolates, we obtained 197 ITS genotypes. The GenBank VRT752271 cost accession numbers and the GenBank BLAST top score similarity of these YH25448 price ITS genotypes, excluding uncultured and environmental sequences, are listed in Online Ressource 2. We used a 99 % sequence BLAST similarity

threshold Tyrosine-protein kinase BLK for species delimitation (Gazis et al. 2011) even though previous fungal endophyte-related studies have used a lower threshold (≤98 %; Higgins et al. 2011; Neubert et al. 2006; O’Brien et al. 2005; Sánchez et al. 2007; Sánchez et al. 2008; U’Ren et al. 2010). The ITS sequence of the fungal isolate acwVHB69/4 (Online Resource 2) was 100 % similar with the ITS GenBank sequences of six different species of Cladosporium, including C. subtilissimum. In those cases where ITS rDNA sequences data discriminated more than one taxa, we used the prefix ‘cf’ in the fungal name (e.g. Cladosporium cf subtilissimum, Online Resource 2, Table 1). On the other hand, we also recovered variable ITS genotypes that corresponded to the same species under the blast results. In these cases we used the name derived from GenBank, accepting that this was not aligned with extype. For Alternaria, we recovered ITS rDNA genotypes for 216 isolates that differed only in the length of a T-repeat at the end of the ITS2. Sequences with 6, 7 or 8 T-repeats were respectively 100 % similar with GenBank sequences of Alternaria alternata, A. arborescens, and A. mali (Online resource 2).