Data Sheet 3_Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly.csv

BackgroundOgataea parapolymorpha DL-1 is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome and methylome analysis of Ogataea parapolymorpha DL-1 using long-read sequencing technology. The research builds upon previous short-read sequencing efforts, revealing enhancements in genome assembly and epigenomic insights.
MethodsWe used long-read sequencing technology to achieve a telomere-to-telomere (T2T) genome assembly of Ogataea parapolymorpha DL-1. High-quality reads were obtained and assembled de novo, followed by polishing to enhance accuracy. The genome was analyzed to identify coding genes, telomeric motifs, rRNA genes, and methylation patterns, including the detection of 5mC and 6 mA modifications. Epigenetic features were further assessed and validated through liquid chromatography-mass spectrometry.
ResultsKey findings include the absence of 5 mC DNA modification and the presence of 6 mA in the genome, unusual telomere regulation mechanism based on the addition of non-telomeric dT and the introduction of long-read enhanced telomere-to-telomere assembly.
ConclusionThis work provides deeper insights into the yeast’s genome organization and methylation patterns, contributing to the understanding of its genetics and therefore potential biotechnological applications.

背景
多形Ogataea（Ogataea parapolymorpha）DL-1是一种多功能耐热微生物，在生物技术领域拥有广泛应用场景，尤其可用于重组蛋白生产、甲醇代谢及过氧化物酶体功能的相关研究。本研究依托长读长测序技术，对多形Ogataea DL-1开展了全基因组与甲基化组的综合分析。本研究在既往短读长测序研究的基础上，实现了基因组组装质量的优化，并获得了新的表观基因组学认知。

方法
本研究采用长读长测序技术，完成了多形Ogataea DL-1的端粒到端粒（telomere-to-telomere, T2T）基因组组装。研究获取高质量测序读段并进行从头组装，随后通过抛光步骤提升组装准确性。对组装完成的基因组开展分析，以鉴定编码基因、端粒基序、核糖体RNA（rRNA）基因以及甲基化模式，其中涵盖5-甲基胞嘧啶（5mC）与6-甲基腺嘌呤（6mA）两种修饰的检测。通过液相色谱-质谱联用技术（liquid chromatography-mass spectrometry, LC-MS）对表观遗传特征进行进一步评估与验证。

结果
本研究的核心发现包括：基因组中不存在5mC DNA修饰，但存在6mA修饰；存在一种基于非端粒dT添加的非常规端粒调控机制；以及借助长读长测序技术实现了优化的端粒到端粒基因组组装。

结论
本研究为该酵母的基因组组织与甲基化模式提供了更深入的认知，有助于深化对其遗传学特性的理解，进而为其潜在的生物技术应用提供理论支撑。