A Chromosome-Level Genome Assembly of <em>Rhizopus stolonifer</em> from Passion Fruit

Flower rot of passion fruit, caused by Rhizopus stolonifer, is an emerging disease that threatens commercial cultivation of passion fruit by reducing yield and fruit quality. To investigate the molecular basis of pathogenicity and provide genomic resources for disease management, we generated a high-quality, chromosome-level genome assem-bly of R. stolonifer isolate PRFJ02 using PacBio HiFi sequencing combined with Hi-C chromatin conformation capture. The assembled genome spanned 48.2 Mb across 11 chromosomes, with a BUSCO completeness of 95.2%, and encoded 11,885 pro-tein-coding genes. Functional annotation revealed a strong metabolic capacity, includ-ing 422 carbohydrate-active enzymes (CAZymes) involved in carbohydrate degradation and modification. Effector prediction identified 274 candidate apoplastic effectors, highlighting potential roles in host–pathogen interactions. Whole-genome phylogenetic analysis across 48 Rhizopus genomes confirmed that R. stolonifer forms a distinct phy-logroup, separate from R. microsporus, R. delemar, and R. arrhizus. Comparative orthol-ogous clustering identified conserved core gene sets alongside clusters unique to PRFJ02 enriched in functions related to carbohydrate binding, DNA recombination, and energy metabolism. This underscores the genetic adaptation and pathogenicity of R. stolonifer. Together, these findings provide novel insights into the molecular mechanisms un-derlying flower rot in passion fruit and establish a valuable genomic framework for developing targeted disease management strategies.