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Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Seedson 添加于 2012-6-4 04:29 | 1650 次阅读 | 0 个评论

作者
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo M-J, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS
摘要
Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single Escherichia coli and Staphylococcus aureus cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many E. coli cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.
详细资料
- 文献种类:期刊
- 期刊名称: Nature Biotechnology
- 期刊缩写: Nat Biotechnol
- 期卷页: 2011年
- ISBN: 1087-0156
相关链接 DOI URL
附件
Efficient de novo assembly of single-cell bacterial genomes from short-read data