論文

査読有り 国際誌
2018年2月1日

Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes.

Scientific reports
  • Masato Kogawa
  • ,
  • Masahito Hosokawa
  • ,
  • Yohei Nishikawa
  • ,
  • Kazuki Mori
  • ,
  • Haruko Takeyama

8
1
開始ページ
2059
終了ページ
2059
記述言語
英語
掲載種別
DOI
10.1038/s41598-018-20384-3

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.

リンク情報
DOI
https://doi.org/10.1038/s41598-018-20384-3
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/29391438
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794965
ID情報
  • DOI : 10.1038/s41598-018-20384-3
  • PubMed ID : 29391438
  • PubMed Central 記事ID : PMC5794965

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