Rust fungi are a group of pathogens infecting a variety of species including important crops. Stripe rust (Puccinia striiformis f.sp. tritici) is a fungal pathogen specialized in infecting wheat. Different lineages of the fungus have been introduced to Australia in the last decades and five lineages have been responsible for the majority of stripe rust infections. Relative frequency of these lineages and pathotypes causing disease changed over time with more recently introduced lineages replacing older introductions. Recent data suggests that isolates do not only differ in terms of susceptibility to specific plant resistance genes but also in their “aggressiveness” in causing disease. Stripe rust, as many other basidiomycetes, partitions individual haplotype genome copies into discrete nuclei. We utilized long read sequencing (PacBio HiFi and Oxford Nanopore (ONT) duplex reads) combined with HiC to generate haplotype phased genomes for the five different Australian lineages. To characterize haplotype specific infection programs, we performed long-read ONT cDNA sequencing comparing different time points during wheat infection for each lineage. Analysing both, differences as the infection progresses, as well as differences between the distinct lineages on a genomic and transcriptomic level will improve our fundamental understanding of how the presence of multiple nuclei contributes to disease severity and rapid adaptation to variable and changing agricultural environments.