A chromosome-level genome assembly of Rhizopus stolonifer associated with passion fruit flower rot

Flower rot of passion fruit, caused by Rhizopus stolonifer, is an emerging disease that threatens commercial cultivation by reducing yield and fruit quality. Here, we present a chromosome-level genome assembly of R. stolonifer isolate PRFJ02, generated using PacBio HiFi sequencing combined with Hi-C chromatin conformation capture. The assembled genome spans 48.2 Mb across 11 chromosomes, with 98.9% completeness, and encodes 11,737 protein-coding genes. Functional annotation revealed a diverse repertoire of genes involved in metabolism, signal transduction, and protein processing, reflecting the organism's broad biological capacity. Comparative genomic analyses across related Rhizopus species identified a conserved core gene set alongside lineage-specific gene clusters, and showed that PRFJ02 exhibits substantial gene family contraction relative to other genomes, with comparatively limited gene family expansion. Comparative effector analysis revealed a limited core effector gene set and a predominance of genome-specific effectors. Only a small number of effectors were shared exclusively among plant-infecting strains, suggesting that differences in effector repertoires alone do not explain differences among plant-infecting isolates. Analysis of carbohydrate-active enzymes (CAZymes) showed that glycoside hydrolases were the dominant class in secreted enzyme repertoire in PRFJ02 and other Rhizopus genomes. In PRFJ02, several CAZyme families, including glycoside hydrolase family GH28 and polysaccharide lyase families PL1 and PL41, were enriched, highlighting enzymes associated with pectin degradation. Together, these results provide a high-quality genome resource for R. stolonifer and new insights into its genomic features and secreted enzyme repertoire. They also provide a basis for future studies on the biology and management of flower rot in passion fruit.