Faulk Christopher
Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota.
bioRxiv. 2023 Jan 25:2023.01.25.525540. doi: 10.1101/2023.01.25.525540.
Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.
基因组快速扫描被定义为覆盖度低于0.05X的低通量测序，通常用于线粒体基因组回收和物种鉴定。长读长纳米孔测序仪能够同时读取DNA序列和甲基化情况，并且可以对样本进行多重分析以实现低成本的基因组快速扫描。在此，我将纳米孔测序展示为一个用于全局DNA甲基化和转座子评估的高精度平台。在仅0.001X的覆盖度下，即30兆碱基的读取量，准确率低于1%。生物学和技术重复验证了高精度。对40种脊椎动物物种进行快速扫描揭示了与全基因组亚硫酸氢盐测序一致的全局甲基化保守模式，平均映射率超过97%。基因组大小与全局DNA甲基化直接相关，解释了其44%的方差。仅需0.0001X的覆盖度，即3兆碱基的读取量，就可以在小鼠和灵长类动物中获得准确的短散在核元件（SINE）和长散在核元件（LINE）转座子甲基化情况。样本多重分析、现场便携性以及该仪器的低价格相结合，使得用于DNA甲基化的基因组快速扫描成为一种从生态学到流行病学、可供资源匮乏群体使用的表观遗传学评估方法。
