Genome assemblies of Puccinia striiformis f. sp. tritici isolates DK06_00 and NL72067

Genome assemblies of two Puccinia striiformis f.sp. tritici isolates belonging to the PstS0 lineage (DK06_00 and NL72067). Reads were basecalled with dorado (v0.7.2) and the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads were subsequently error corrected using herro (v1) (Stanojevic et al., 2024) and both raw and error corrected reads used as input for genome assembly using verkko v2.0 (Rautiainen et al., 2023). Genome assemblies were scaffolded with RagTag (Alonge at al., 2022) using the Pst104E genome as reference (Tam et al., 2025). After scaffolding both assemblies contained 36 chromosome scale contigs including telomeres on both ends of each chromosome. Information on DK06_00 and NL72067 can be found under NCBI Biosample accessions: SAMN57474761, SAMN57474762. We provide updated assemblies and annotations for isolate Pst104E (Tam et al., 2025). We reassembled the Pst104E genome (Pst104Ev4) using previously published ONT simplex reads and Hi-C with hifiasm v0.25.0-r726 (--ont --dual-scaf --telo-m), which closed two gaps compared to the last version. We reannotated genes using ONT cDNA and Illumina RNA-seq combined as previously described in (Tam et al., 2025), with a few adaptations associated with infection-only transcripts following the protocols in (Sperschneider et al. 2023) to rescue more putative secretome genes.