In silico functional annotation based on protein signatures and homologies allowed us to assign a function to 43% of the 11,839 predicted proteins. A total of 2714 sequences (22.9%) had no homologies within the NCBI nonredundant protein database and did not include any known protein domain. These represent either species-specific genes of Z. tritici or incorrectly predicted genes. Given the fact that 55% of these have RNA-seq support, we considered that the majority of these novel genes must be correctly predicted. Characterization of the Z. tritici secretome yielded comparable results to the previously reported Z. tritici secretome (Morais Do Amaral et al. 2012), representing 874 secreted proteins including 441 small, secreted proteins (SSPs), i.e., with a size inferior to 300 amino acids (Table 1). SSPs of Z. tritici have, on average, 2.8-times more cysteine residues compared to the whole proteome (data not shown supporting an extracellular role) (Fass 2012).