Spatial Vulnerabilities of the Escherichia coli Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing
Spatial Vulnerabilities of the Escherichia coli Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing
复制标题
通过改进的双工测序揭示大肠杆菌基因组对自发突变的空间脆弱性
DOI：
10.1534/genetics.118.301345
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发表时间：
2018-10-01
期刊：
影响因子：
3.3
通讯作者：
Li, Zhiguang
中科院分区：
文献类型：
--
作者：
Zhang, Xiaolong;Zhang, Xuehong;Li, Zhiguang
由于自发突变在进化和病理过程中的重要作用，利用新一代测序技术对自发突变的研究引起了广泛关注。然而，这些研究仅关注在长期（可能是数年）培养期间通过许多代积累的突变，而不是以非常低的频率发生的新鲜产生的突变。在这项研究中，我们建立了一种分子条形码深度测序策略来检测细菌细胞培养物基因组中的低丰度自发突变。15份大肠杆菌细胞培养样品中的全基因组自发突变具有高置信度（P < 0.01）。我们还开发了一种基于游程编码算法的热点调用方法，以找到易受自发突变影响的基因组区域。突变的热点似乎在细菌样品中高度保守。对这些区域的进一步生物学注释表明，大多数自发突变位于基因组的重复结构域或非功能结构域，这表明存在某种机制，可以以某种方式防止关键基因区域突变的发生。这项研究提供了在无需长期培养的单一扩增过程中突变发生和谱的更真实的情况。
Investigation of spontaneous mutations by next-generation sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long-term (possibly be years of) culturing, but not the freshly generated mutations that occur at very low frequencies. In this study, we established a molecularly barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 Escherichia coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot-calling approach based on the run-length encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra in a single expansion process without long-term culturing.