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Background: HC-toxin, a cyclic tetrapeptide, is a virulence determinant for the plant pathogenic fungus Cochliobolus carbonum. It was recently discovered that another fungus, Alternaria jesenskae, also produces HC-toxin. Results: The major genes (collectively known as AjTOX2) involved in the biosynthesis of HC-toxin were identified from A. jesenskae by genomic sequencing. The encoded orthologous proteins share 75-85% amino acid identity, and the genes for HC-toxin biosynthesis are duplicated in both fungi. The genomic organization of the genes in the two fungi show a similar but not identical partial clustering arrangement. A set of representative housekeeping proteins show a similar high level of amino acid identity between C. carbonum and A. jesenskae, which is consistent with the close relatedness of these two genera within the family Pleosporaceae (Dothideomycetes). Conclusions: This is the first report that the plant virulence factor HC-toxin is made by an organism other than C. carbonum. The genes may have moved by horizontal transfer between the two species, but it cannot be excluded that they were present in a common ancestor and lost from other species of Alternaria and Cochliobolus. [ABSTRACT FROM AUTHOR]