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The genus Alternaria includes both plant-pathogenic and saprophytic species, which may affect crops in the field or cause harvest and postharvest decay of plant products. The taxonomy of the genus Alternaria is not well-defined yet. A polyphasic approach based on morphological features, phylogeny and toxin profiles could be the key to a correct identification at species level and the evaluation of mycotoxin risks associated with fungal contamination. Species of Alternaria are known to produce many metabolites, mostly phytotoxins, which play an important role in the pathogenesis of plants. However, certain species, in particular the most common one A. alternata, are capable of producing several mycotoxins in infected plants and/or in agricultural commodities. The major Alternaria mycotoxins belong to three structural classes: the tetramic acid derivative, tenuazonic acid; the dibenzopyrone derivatives, alternariol …