Bai Yu-Ting, Sharma Awkash, Xiang Qian, Tian Li-Yan, Li Ke-Jing, Guo Bao-Ying, Qi Lei, Zheng Dao-Qiong
Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316021, China.
Ocean College, Zhejiang University, Zhoushan, 316021, China.
BMC Genomics. 2025 Mar 25;26(1):297. doi: 10.1186/s12864-025-11479-z.
Understanding the mechanisms of genetic evolution in marine yeasts is essential for their ecological and biotechnological applications. Scheffersomyces spartinae, an ascomycetous yeast species, characterized by its remarkable robustness and carbon source utilization capability, has garnered significant attention for its biotechnological potential.
In this study, we investigated the spontaneous and induced genomic alterations of the marine yeast S. spartinae under various conditions. Through mutation accumulation experiments combined with whole-genome sequencing, we revealed that the rates of spontaneous single nucleotide variations and small insertions and deletions were 6.3 × 10⁻¹¹ and 1.4 × 10⁻¹¹ per base pair per cell division, respectively, in S. spartinae. The predominant type of base substitution was C-to-T or G-to-A, likely induced by cytosine deamination. Template slippage during DNA replication emerged as the primary cause of small InDels. 50 J/m UV treatment elevated the SNV rate by 124-fold, with C-to-T substitutions occurring at the 5'-TC-3' motif and T-to-C substitutions at the 5'-TT-3' motif being the most prominent features. Exposure to 50 µg/mL Zeocin resulted in 76-fold and 71-fold increases in the rates of SNVs and InDels, respectively, with frequent T-to-A mutations and T deletions occurring at the 5'-GT-3' motifs. Heat stress at 37 °C increased the SNVs and InDels rates to 1.4 × 10⁻¹⁰ and 7.5 × 10⁻¹¹ per base pair per cell division. Notably, this study demonstrated that large deletions and duplications (> 1 kb) and aneuploidies are less likely to occur in S. spartinae compared to other yeast species, suggesting that this organism is less tolerant to large-scale genomic alterations. In contrast, we observed a marked decrease in rDNA copy numbers when S. spartinae cells were cultivated at elevated temperature conditions. This finding indicates that variations in rDNA copy numbers might act as an adaptive strategy for yeasts in response to fluctuating temperatures.
Our findings provide novel insights into the patterns and genetic mechanisms underlying genomic evolution in yeasts.
了解海洋酵母的遗传进化机制对于其生态和生物技术应用至关重要。斯帕蒂纳舍弗酵母是一种子囊菌酵母物种，以其显著的稳健性和碳源利用能力为特征，因其生物技术潜力而备受关注。
在本研究中，我们调查了海洋酵母斯帕蒂纳舍弗酵母在各种条件下的自发和诱导基因组改变。通过结合全基因组测序的突变积累实验，我们发现斯帕蒂纳舍弗酵母中自发单核苷酸变异以及小插入和缺失的速率分别为每细胞分裂每碱基对6.3×10⁻¹¹和1.4×10⁻¹¹。碱基替换的主要类型是C到T或G到A，可能是由胞嘧啶脱氨诱导的。DNA复制过程中的模板滑动是小插入缺失的主要原因。50 J/m的紫外线处理使单核苷酸变异率提高了124倍，5'-TC-3'基序处发生C到T替换以及5'-TT-3'基序处发生T到C替换是最显著的特征。暴露于50 μg/mL博来霉素分别导致单核苷酸变异率和插入缺失率增加76倍和71倍，5'-GT-3'基序处频繁发生T到A突变和T缺失。37°C的热应激使每细胞分裂每碱基对的单核苷酸变异率和插入缺失率分别增加到1.4×10⁻¹⁰和7.5×10⁻¹¹。值得注意的是，本研究表明与其他酵母物种相比，斯帕蒂纳舍弗酵母中大片段缺失和重复（>1 kb）以及非整倍体发生的可能性较小，这表明该生物体对大规模基因组改变的耐受性较低。相反，当斯帕蒂纳舍弗酵母细胞在高温条件下培养时，我们观察到核糖体DNA拷贝数显著减少。这一发现表明核糖体DNA拷贝数的变化可能作为酵母应对温度波动的一种适应性策略。
我们的研究结果为酵母基因组进化的模式和遗传机制提供了新的见解。
