Experimental insights into genome reconstruction driven by horizontal transfer of supernumerary chromosomes in Magnaporthe oryzae

Summary Many pathogenic fungi display ‘two‐speed genome’, with the fast‐evolving genomic compartments enriched with repetitive sequences, particularly the transposons, which have been shown to drive the variation of pathogenicity‐associated genes. Supernumerary chromosomes (SCs) are known to facilitate genomic variation in fungal pathogens, but their specific role in such processes remains understudied. In this study, we assessed the transferability of SCs between asexual Magnaporthe oryzae strains during co‐culture and co‐infection, and investigated their role in genome reconstruction through experimental evolution assays. We found that SCs could be horizontally transferred between M. oryzae strains and revealed frequent structural variations facilitated by SCs, including deletions, duplications, translocations, and SC‐core chromosome recombinations during and after horizontal transfer. Remarkably, all observed intra‐ and inter‐chromosome rearrangements were confined to core chromosome ends and SCs, indicating a robust role of SCs in facilitating genetic exchange within fast‐evolving genomic compartments. Additionally, SC carrying the avirulence gene AvrPik E modulates M. oryzae virulence against Pikh rice through horizontal transfer, loss of whole SC, and segmental deletions. Our findings establish SCs as critical players in shaping the diversity and dynamics of the pathogenic fungal genomes, highlighting them as a cradle for the variation of pathogenicity‐associated genes.