Multi-omics analysis reveals the mechanism underlying the dimorphic formation of Saccharomycopsis fibuligera during dough fermentation

To unravel the mechanism underlying the dimorphic formation of Saccharomycopsis fibuligera during dough fermentation, we assembled a high-quality chromosome-scale genome and conducted comparative genomic analysis. Furthermore, we examined the differences between the yeast-like cells and hyphae at both transcriptome and metabolome levels. The completed S. fibuligera ACX0001 genome of 19.29 Mb comprised seven chromosomes and contained 6115 predicted protein-coding genes. Comparative genomic analysis revealed that S. fibuligera possessed 51 unique gene families comprising 85 annotated genes. The advantageous genes related to carbon metabolism pathway were accumulated in S. fibuligera during evolution, including the unique genes encoding glycosyl hydrolases such as glucan endo-1,3-β glucosidase, which distinguished it from the other yeasts. Transcriptomic and metabolomic analysis identified 568 differentially expressed genes and 109 differentially abundant metabolites between the yeast-like cells and hyphae, respectively. In response to the dough environment, S. fibuligera activated the expression of the glucan endo-1,3-β glucosidase, which can soften the cell wall and promote germination of yeast-like cells. Simultaneously, the flux of acetyl-CoA was redirected towards fatty acid and steroid biosynthesis in S. fibuligera, which influenced the production of quorum-sensing molecules, thereby contributing to the dimorphic transition. Therefore, the dimorphic growth of S. fibuligera was collectively governed by the glycosyl hydrolase family genes, central carbon metabolism, and quorum-sensing molecules. This study provides a theoretical foundation for the potential application of S. fibuligera in food industry.