The genome of Z. tritici (isolate IPO323) was sequenced and annotated by the Joint Genome Institute (JGI) and provides one of the best-assembled eukaryotic genomes with 21 complete chromosomes sequenced from telomere to telomere (Goodwin et al. 2011). Of the 21 chromosomes, eight are considered accessory chromosomes because they can be lost during meiosis without any apparent effect on fitness in sexual progenies (Wittenberg et al. 2009). The functional relevance of these accessory chromosomes is so far not known. They contain a higher proportion of repetitive DNA, encode fewer genes (Goodwin et al. 2011), and show a dramatically lower level of transcription compared to the core chromosomes (Kellner et al. 2014). The previously generated annotation predicted more than 10,000 genes in the genome of IPO323. The pipeline applied for the annotation used several gene predictors including putative full-length genes from EST cluster consensus sequences (Goodwin et al. 2011). Nevertheless, this gene annotation comprises many incomplete gene models (14%) without start and/or stop codons.