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The increasing multi-drug resistance observed in the turfgrass pathogenClarireediaspp. has emerged as a critical issue. Understanding the mechanisms underlying fungicide resistance is crucial to address this challenge. This study focuses on comparing a highly propiconazole-resistant isolate ofClarireedia jacksonii, HRI11, with a sensitive isolate, HRS10. Genomes were sequenced using the Oxford Nanopore MinION sequencing platform, and hybrid assembly was performed using this data and existing Pacific Biosciences long reads and Illumina short reads. HRI11 genome assembly represents the most contiguous and complete genome assembly reported forClarireediato date, spanning 43.6 MB with 12,831 predicted protein-coding genes across 51 scaffolds. In contrast, the HRS10 had an assembly size of 39.6 MB and encoded 12,161 putative proteins distributed over 100 scaffolds. While the two isolates share substantial sequence similarity and overall protein content, the fungicide resistance observed in HRI11 appears to arise primarily from genetic variants, particularly in genes encoding transcription factors, transporters, and fungicide target genes. These genetic variants establish a foundational resistance level against fungicides. Furthermore, induced resistance in HRI11 involves increased expression of proteins that facilitate fungicide efflux, thereby optimizing energy allocation during fungicide exposures. Together, these mechanisms-inherent genetic variation and adaptive transcriptional responses-contribute to the heightened resilience of HRI11 under fungicide treatment. 

Abstract Traditional fermented foods often contain specialized microorganisms adapted to their unique environments. For example, the filamentous mold Aspergillus oryzae, used in saké fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae, used in soybean-based fermentations like miso and shochu, is hypothesized to have been domesticated from Aspergillus parasiticus. Here, we examined the effects of long-term A. sojae use in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 17 A. sojae and 24 A. parasiticus genomes (23 of which were sequenced for this study), alongside phenotypic traits of 9 isolates. Aspergillus sojae formed a distinct, low-diversity population, suggesting a recent clonal expansion. Interestingly, a population of A. parasiticus was more closely related to A. sojae than other A. parasiticus populations. Genome comparisons revealed loss-of-function mutations in A. sojae, notably in biosynthetic gene clusters encoding secondary metabolites, including the aflatoxin cluster. Interestingly though, A. sojae harbored a partial duplication of a siderophore biosynthetic cluster. Phenotypic assays showed A. sojae lacked aflatoxin production, while it was variable in A. parasiticus isolates. Additionally, certain A. sojae strains exhibited larger colony diameters under miso-like salt conditions. These findings support the hypothesis that A. parasiticus is the progenitor of A. sojae and that domestication significantly reduced genetic diversity. Future research should explore how wild and food-associated strains influence sensory attributes and microbial community dynamics in fermented soy products.