Chromosome-resolved genome of the rice blast fungus Magnaporthe oryzae KJ201 enables comparative analysis of genome architecture and pathogenicity-associated loci

Rice blast, caused by Magnaporthe oryzae , threatens rice production and is a model for fungal pathogenicity. The Korean rice isolate KJ201 has supported extensive functional, transcriptomic, and epigenomic research, but its fragmented reference genome has limited chromosome-scale interpretation. PacBio HiFi and Hi-C sequencing produced a 44.8 Mb assembly comprising seven chromosome-scale scaffolds and three mini-scaffolds, with an N50 of 6.5 Mb and 98.5% complete BUSCOs. Comparative analysis with 17 public M. oryzae genomes grouped KJ201 with P131 and O-135, separately from the 70-15/Guy11-containing rice subclade. The seven core chromosomes were broadly conserved, whereas localized chromosome-terminal differences and variable breakpoint burdens characterized the sampled comparisons. Gene-family content was largely conserved. Secreted effector candidates showed elevated local repeat density, and 61 ORF-disrupting pathogenicity-associated loci from the KJ201 Agrobacterium-mediated insertional mutant collection were mapped across all seven major chromosomes. This assembly connects comparative chromosome organization, candidate effector genomic context, and legacy mutant phenotypes in a native KJ201 reference.