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 placed KJ201 with the East Asian rice isolates P131 and O-135, apart from the 70 − 15/Guy11 lineage. The seven core chromosomes were broadly conserved, whereas localized chromosome-terminal differences and breakpoint patterns differentiated rice subclades and host-associated groups. Gene-family content was largely conserved. Secreted effector candidates showed elevated local repeat density, and 57 ORF-disrupting pathogenicity loci from the KJ201 Agrobacterium-mediated insertional mutant collection were mapped across all seven major chromosomes. This assembly links East Asian lineage architecture, dynamic effector-associated regions, and experimentally derived pathogenicity loci in a native rice blast genome.