Puccinia triticina isolate Race 9, SBDGK, Phased Genome Assembly

Presented here are the two phased genomes of the dikaryotic fungus, Puccinia triticina, isolate Race9 ( SBDGK, 1959) and their annotation, part of the North American Pan-genome Rust initiative. Haplotype A: Phased genome assembly of Puccinia triticina Race 9 (isolate SBDGK). This record represents Haplotype A, containing 18 reconstructed chromosomes. The assembly was generated using Oxford Nanopore PromethION long-reads and Illumina Hi-C scaffolding, phased via custom Necat and HapCUT2 pipelines (to be published soon) to resolve the HD:PtE/W5 and PR:STE3.2 mating-type loci. Bioproject: PRJNA1298920 Haplotype B: Phased genome assembly of Puccinia triticina Race 9 (isolate SBDGK). This record represents Haplotype B, containing 18 reconstructed chromosomes. The assembly was generated using Oxford Nanopore PromethION long-reads and Illumina Hi-C scaffolding, phased via custom Necat and HapCUT2 pipelines (to be published soon) to resolve the HD:PtE/W6 and PR:Ste3.3 mating-type loci. Bioproject: PRJNA1298919Haplotype B was used for mapping and GWAS in "Avirulence genes identified through linkage mapping and region-specific association studies in the wheat leaf rust pathogen Puccinia triticina" (Liu, 2025) using previous called chromosome numbers. The fasta's here reflect updated chromosomal numbers along with the associated mapping conversion text files. NCBI and ENA links to the genome and annotation will be updated when available. Accessions for Raw Data used for assembly and annotation:Nanopore: ERR16003188Hi-C: ERR16003190WGS: SRR29057043RNA-seq: SRR29057033