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首页> 外文期刊>Scientific reports. >Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes
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Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes

机译：通过清洗和共组装单细胞扩增基因组，从未培养的微生物中获得高质量的基因组草图

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Single-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences. Here, we describe Cleaning and Co-assembly of a Single-Cell Amplified Genome (ccSAG), a novel analytical workflow to obtain composite single-cell genomes with elimination of sequence errors. By the integration of ccSAG with a massively parallel single-cell genome amplification platform based on droplet microfluidics, we can generate multiple SAGs and effectively integrate them into the composite genomes quality equivalent to the data obtained from bulk DNA. We obtained two novel draft genomes from single gut microbial cells with high completeness (96.6%) and extremely low contamination (1.25%). Moreover, we revealed the presence of single nucleotide polymorphisms in the specific gene by sequence comparison at the single-cell level. Thus, the workflow yields near-complete genomes from uncultured microbes, and enables analyses of genetic heterogeneity within identical strains.
机译：单细胞基因组学是从未经培养的微生物中获取基因组的直接方法。但是，从单细胞扩增基因组（SAG）读取的序列包含明显的偏好和嵌合序列。在这里，我们描述了单细胞扩增基因组（ccSAG）的清洁和协同组装，这是一种新颖的分析工作流程，可获取消除序列错误的复合单细胞基因组。通过将ccSAG与基于液滴微流体的大规模并行单细胞基因组扩增平台整合，我们可以生成多个SAG，并将其有效整合到与从大宗DNA获得的数据相当的复合基因组质量中。我们从单个肠道微生物细胞中获得了两个新颖的基因组草图，它们具有很高的完整性（> 96.6％）和极低的污染（<1.25％）。此外，我们通过单细胞水平的序列比较揭示了特定基因中单核苷酸多态性的存在。因此，该工作流程可从未培养的微生物中获得近乎完整的基因组，并能够分析同一菌株内的遗传异质性。

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