Emergence of a hybrid PKS-NRPS secondary metabolite cluster in a clonal population of the rice blast fungus Magnaporthe oryzae. Pyricularia oryzae

Secondary metabolite (SM) clusters are rapidly evolving regions in the fungal genome. However, the driving force and genetic mechanism of SM cluster diversification in the context of host-pathogen interactions remain largely unknown. Here, we present a recent duplication of an avirulent gene-containing SM cluster, ACE1, in the genome of the rice blast fungus Magnaporthe oryzae. We demonstrate that the ACE1 cluster is specifically duplicated in a dominant clonal lineage of the M. oryzae population in indica rice-growing areas. Chromosome-level genome sequences show that the frequent duplication and rearrangement of the ACE1 cluster in this clonal population is mediated by transposable elements. Together with the rice subspecies distribution of the M. oryzae population, these results highlight rice subspecies as a driving force of fungal SM cluster diversification in the context of host-pathogen interactions and demonstrate transposable element-mediated whole-cluster duplication as a genetic mechanism that shapes fungal SM cluster diversification.