These three fungal wheat pathogens all possess a known virulence gene, ToxA, which has been shared between the three species via horizontal gene transfer. Previous works indicated that this virulence gene is closely associated with repetitive regions of the genome, which with short read data only, are difficult to assemble. This study used long read sequencing to generate near-complete genome assemblies for several representatives of two of the three species. These assemblies provide the most comprehensive look, thus far, at the genomic context of this important gene. They also provide some insight into the extent of horizontal gene transfer between the three species.</p><p>All raw data was generated using long-read sequencing technology either PacBio SMRT or Oxford Nanopore. Genomes were assembled with Canu and polished using short read data when available. There are two species included in this Bio-project, Bipolaris sorokinana (4 isolates) and Parastagonospora nodorum (2 isolates). There is a third species that is included in this study (Pyrenophora tritici-repentis), however we have used previously published data for this species. We used short read data for one isolate of P. tritici-repentis, which is also available here in this Bioproject.