The gene and TE annotation of the four Zymoseptoria species genomes coupled with preliminary comparative analysis allowed us to highlight interesting features relevant to the biological life traits of these organisms. Establishment of homologous sequence families across the four species showed that a large part of genes are shared between two or more species and that the major difference of gene content relies on orphan genes. These orphan genes, in all four species, are significantly enriched in putative pathogenicity-related genes and potentially play a role in the determination of host specificity. Similar presence–absence patterns of pathogenicity-related genes were shown to be strong determinants of host range in plant pathogens, e.g., between lineages of the rice blast pathogen Magnaporthe oryzae, the wilt pathogen Verticillium dahliae, and lineages of the Leptosphaeria maculans–Leptosphaeria biglobosa species complex (Couch et al. 2005; de Jonge et al. 2012; Grandaubert et al. 2014). Similarly, comparison of TE families showed a majority of species-specific sequences; this underlies the fact that each species genome has been widely invaded after the species divergence. We speculate that TEs may have played a role in host specialization by the acquisition or modification of pathogenicity-related traits. Also, large TE-rich regions could have played a role in speciation through the suppression of homologous recombination in chromosomal regions with inversions or translocations as proposed for the Leptosphaeria maculans–Leptosphaeria biglobosa species complex (Grandaubert et al. 2014). In Dhillon et al. (2014), the authors stated that several genes with putative pathogenicity-related functions were found to be associated with TEs. Preliminary analyses of genes and TEs tend to show that orphan genes are located significantly closer to TEs than other nonorphan genes (J. Grandaubert, unpublished data). TEs thus may play a role in the origin and evolution of these genes.