Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae

The halotolerant yeast Scheffersomyces spartinae, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of S. spartinae named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized S. spartinae YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast Saccharomyces cerevisiae, S. spartinae YMxiao exhibited greater tolerance to various stressful conditions. Furthermore, S. spartinae YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of S. spartinae YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between S. spartinae strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in S. spartinae strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in S. spartinae. Our findings not only enhance our understanding of the S. spartinae genome but also provide a foundation for future research into its potential biotechnological applications. KEY POINTS: • The unique phenotypes and genetic characteristics of S. spartinae were disclosed. • Comparative genomics showed vast genetic variations between S. spartinae strains. • Genetic manipulation protocol was established for S. spartinae strain.