Chromosome-scale and nuclear haplotype-phased assemblies of two Puccinia striiformis f. sp. tritici isolates, Pst239E (PstS10) and PstS7 The fully haplotype-phased reference genome for an Australian sampled Pst239E isolate, which belongs to the PstS10 lineage, was generated using PacBio HiFi and Oxford Nanopore Technology (ONT) R10.4-based long-reads and Hi-C as input for Verkko hybrid genome assembler (Rautiainen et al., 2023). The haplotype-phased reference genome of PstS7 used ONT R10.4.1 simplex reads and Hi-C with hifiasm --ont (Cheng et al., 2025). Please see the assembly quality statistics table in the manuscript. The assemblies have also been submitted to NCBI with the following accession, waiting to be processed and released. Pst239E (PstS10) PRJNA1260730 : Puccinia striiformis f. sp. tritici haplotype 1 genome sequencing (haplotype A) PRJNA1260729 : Puccinia striiformis f. sp. tritici haplotype 2 genome sequencing (haplotype B) PstS7 PRJNA1260732 : Puccinia striiformis f. sp. tritici haplotype 1 genome sequencing (haplotype A) PRJNA1260731 : Puccinia striiformis f. sp. tritici haplotype 2 genome sequencing (haplotype B)