Illuminating Olea europaea L. endophyte fungal community

[Display omitted] •Fungal endophytes from the phyllosphere of five olive cultivars are disclosed.•Different olive cultivars exhibit distinct endophyte communities.•Endophyte communities are mostly shaped by ‘cultivar’ factor rather than ‘organ’.•Olive cultivars display different amounts of fungi with distinct ecological functions.•Tolerance/susceptibility to olive diseases could be explained by fungal community. A wide array of fungal endophytes is known to inhabit plant tissues and were recently recognized as essential for plant health. A better description of the scarcely known endophyte microbiota in olive tree phyllosphere is the first step for elucidating the microbial interactions that lead to olive disease establishment. In this work, the fungal endophytic community of the phyllosphere of different olive tree cultivars (Cobrançosa, Galega vulgar, Madural, Picual, Verdeal Transmontana) is revealed by using a metabarcoding strategy targeting ITS1 barcode. A total of 460 OTUs were obtained, increasing the broad view of fungal endophytes inhabiting the olive tree phyllosphere, in particular yeast endophytes. New endophytes were persistently found in all cultivar tissues. Different olive tree cultivars depicted distinct endophyte communities. Olive cultivars exhibited dissimilar amounts of fungi with distinct ecological functions, which could explain at least in part their differential susceptibility/tolerance to olive diseases.