Draft genome sequence and phenotypic analysis of Pseudozyma sp. SY16 with evidence of binucleate cells

Mannosylerythritol lipids (MELs) are glycolipid biosurfactants that have attracted considerable attention in cosmetic and industrial applications due to their favorable biocompatibility and stability. Pseudozyma sp. SY16 is a promising MEL-producing strain with high production capacity; however, the lack of genomic resources has limited our understanding of its genetic and cellular characteristics and hindered its application in metabolic engineering. In this study, we generated a high-quality draft genome of Pseudozyma sp. SY16 using a hybrid sequencing approach combining long- and short-read sequencing and comprehensively characterized its genomic and cellular features. The 20.2 Mb genome was assembled into 23 nuclear scaffolds and one mitochondrial scaffold, achieving a high BUSCO completeness of 98.9%. Comparative analysis of the MEL biosynthetic genes among closely related species within the family Ustilaginaceae revealed distinct patterns of gene conservation. The mac1 , mac2 , mat1 , mmf1 , and emt1 genes were highly conserved in both gene content and genomic organization among SY16, P. hubeiensis , and Mycosarcoma maydis , whereas only mmf1 was retained in the corresponding regions of P. pruni and P. flocculosa . This pattern suggests lineage-specific retention and loss of MEL biosynthetic genes during the evolution of family Ustilaginaceae. GenomeScope analysis revealed a predominantly single-peaked k-mer distribution, without a clear pattern indicative of either a haploid or diploid genome. Independently, confocal microscopy revealed frequent cells with two spatially separated DAPI-positive signals, consistent with an apparent binucleate morphology. Together, these findings establish a high-quality genomic resource for SY16 and provide new insights into MEL biosynthesis, genome evolution, and cellular organization, providing a foundation for future genetic and metabolic engineering of this non-model yeast toward enhanced MEL production.