ABSTRACT This study explored the genomic alterations in Yarrowia lipolytica , a key yeast in industrial biotechnology, under both spontaneous and mutagen-induced conditions. Our findings reveal that spontaneous mutations occur at a rate of approximately 4 × 10 −10 events per base pair per cell division, primarily manifesting as single-nucleotide variations (SNVs) and small insertions and deletions (InDels). Notably, C-to-T/G-to-A transitions and C-to-A/G-to-T transversions dominate the spontaneous SNVs, while 1 bp deletions, likely resulting from template slippage, are the most frequent InDels. Furthermore, chromosomal aneuploidy and rearrangements occur, albeit at a lower frequency. Exposure to ultraviolet (UV) light, methylmethane sulfonate (MMS), and Zeocin significantly enhances the rates of SNVs and alters their mutational spectra in distinct patterns. Notably, Zeocin-induced SNVs are predominantly T-to-A and T-to-G substitutions, often occurring within the 5′-TGT * −3′ motif ( * denotes the mutated base). Additionally, Zeocin exhibits a higher potency in stimulating InDels compared to UV and MMS. Translesion DNA synthesis is implicated as the primary mechanism behind most Zeocin-induced SNVs and some InDels, whereas non-homologous end joining serves as the main pathway for Zeocin-mediated InDels. Intriguingly, the study identifies the gene YALI1_E21053g , encoding a protein kinase, as negatively associated with Zeocin resistance. Overall, our results not only deepened our knowledge about the genome evolution in Y. lipolytica but also provided reference to develop innovative strategies to harness its genetic potential. IMPORTANCE Yarrowia lipolytica exhibits high environmental stress tolerance and lipid metabolism capabilities, making it a microorganism with significant industrial application potential. In this study, we investigated the genomic variation and evolutionary patterns of this yeast under both spontaneous and induced mutation conditions. Our results reveal distinctive mutation spectra induced by different mutagenic conditions and elucidate the underlying genetic mechanisms. We further highlight the roles of non-homologous end joining and translesion synthesis pathways in Zeocin-induced mutations, demonstrating that such treatments can rapidly confer drug resistance to the cells. Overall, our research enhances the understanding of how yeast genomes evolve under various conditions and provides guidance for developing more effective mutagenesis and breeding techniques.

Yuan-Ru Xiong

Yuan-Chun Fang

Min He

Ke-Jing Li

Lei Qi

Yang Sui

Ke Zhang

Xue-Chang Wu

Liang Meng

Ou Li

Dao-Qiong Zheng

Applied and Environmental Microbiology

应用和环境微生物学 (AEM) 发表的论文对 (A) 应用微生物学，包括生物技术、蛋白质工程、生物修复和食品微生物学，(B) 微生物生态学，包括环境、有机体和基因组微生物学，以及 (C) 做出了重大贡献。 ) 跨学科微生物学，包括无脊椎动物微生物学、植物微生物学、水生微生物学和地球微生物学。

The journal 'Applied and Environmental Microbiology' publishes papers in the following areas: (A) Applied Microbiology, including biotechnology, protein engineering, bioremediation, and food microbiology; (B) Microbial Ecology, covering environmental microbiology, organismal microbiology, and genomic microbiology; (C) Interdisciplinary Microbiology, which includes invertebrate microbiology, plant microbiology, aquatic microbiology, and earth microbiology. These studies have made significant contributions to their respective fields.

《Applied and Environmental Microbiology》期刊发表的论文涵盖以下领域：(A) 应用微生物学，包括生物技术、蛋白质工程、生物修复和食品微生物学；(B) 微生物生态学，涉及环境微生物学、有机体微生物学和基因组微生物学；(C) 跨学科微生物学，包括无脊椎动物微生物学、植物微生物学、水生微生物学和地球微生物学。这些研究对相关领域做出了重要贡献。

Category	Quartile
生物学	2
生物学, 生物工程与应用微生物	2
生物学, 微生物学	3

Patterns of spontaneous and induced genomic alterations in Yarrowia lipolytica

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