From stone fruits to pome fruits: genomic analysis revealed the host adaptation and evolution of Monilinia spp.

Abstract Monilinia fructicola , M. yunnanensis , and M. mumecola are important causative agents of brown rot disease in stone and pome fruits. In this study, we sequenced and assembled the genomes of M. yunnanensis and M. mumecola and compared them with those of four other Monilinia species. Our results revealed an association between host preference and species divergence, with several recently diverged Monilinia species being more frequently associated with pome fruit hosts. Comparative genomic analyses among the different Monilinia species revealed lineage-associated changes in gene family composition, including inferred gene family contractions and the presence/absence variation of a putative polyketide synthase gene cluster. Genes encoding carbohydrate-active enzymes and transporters were relatively conserved across the six species, whereas those encoding secreted proteins showed greater variability and relatively high pairwise Ka/Ks values. During species divergence, hydrophobic surface binding protein A 1 ( MfHsbA1 ) exhibited sequence variations among the Monilinia species, and functional assays indicated that these variations were responsible for inducing necrosis-like symptoms. Overall, this study provides comparative genomic insights into Monilinia species divergence and identifies candidate genomic features potentially involved in host preference, thereby contributing to a better understanding of these destructive plant pathogens.