Different aspects of genome evolution in Z. tritici have been studied using comparative analyses of different Zymoseptoria genomes (Stukenbrock et al. 2010, 2011). A comparative genome study of the reference isolate IPO323 and an isolate of Z. pseudotritici allowed a detailed analysis of genome divergence in coding and noncoding sequences and a comparison of chromosome content and synteny in the two species (Stukenbrock et al. 2010). Multiple genomes were analyzed in a comparative population genomic analysis including Z. tritici, Z. pseudotritici, and Z. ardabiliae to further assess signatures of positive selection and the speciation history of the three species (Stukenbrock et al. 2011). Both studies relied on the previously generated annotation of the Z. tritici reference isolate IPO323, and thereby only described evolution of gene content shared between species.