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De novo assembly of bacterial genomes from single cells
Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of genomes from single cells of bacteria that cannot be cultured. However, genome assembly is challenging because of highly non-uniform read coverage generated by MDA. We describe an improved assembl...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558281/ https://www.ncbi.nlm.nih.gov/pubmed/21926975 http://dx.doi.org/10.1038/nbt.1966 |
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author | Chitsaz, Hamidreza Yee-Greenbaum, Joyclyn L. Tesler, Glenn Lombardo, Mary-Jane Dupont, Christopher L. Badger, Jonathan H. Novotny, Mark Rusch, Douglas B. Fraser, Louise J. Gormley, Niall A. Schulz-Trieglaff, Ole Smith, Geoffrey P. Evers, Dirk J. Pevzner, Pavel A. Lasken, Roger S. |
author_facet | Chitsaz, Hamidreza Yee-Greenbaum, Joyclyn L. Tesler, Glenn Lombardo, Mary-Jane Dupont, Christopher L. Badger, Jonathan H. Novotny, Mark Rusch, Douglas B. Fraser, Louise J. Gormley, Niall A. Schulz-Trieglaff, Ole Smith, Geoffrey P. Evers, Dirk J. Pevzner, Pavel A. Lasken, Roger S. |
author_sort | Chitsaz, Hamidreza |
collection | PubMed |
description | Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of genomes from single cells of bacteria that cannot be cultured. However, genome assembly is challenging because of highly non-uniform read coverage generated by MDA. We describe an improved assembly approach tailored for single cell Illumina sequences that incorporates a progressively increasing coverage cutoff. This allows variable coverage datasets to be utilized effectively with assembly of E. coli and S. aureus single cell reads capturing >91% of genes within contigs, approaching the 95% captured from a multi-cell E. coli assembly. We apply this method to assemble a single cell genome of the uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. These new methods enable acquisition of genome assemblies for individual uncultivated bacteria, providing cell-specific genetic information absent from metagenomic studies. |
format | Online Article Text |
id | pubmed-3558281 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
record_format | MEDLINE/PubMed |
spelling | pubmed-35582812013-01-29 De novo assembly of bacterial genomes from single cells Chitsaz, Hamidreza Yee-Greenbaum, Joyclyn L. Tesler, Glenn Lombardo, Mary-Jane Dupont, Christopher L. Badger, Jonathan H. Novotny, Mark Rusch, Douglas B. Fraser, Louise J. Gormley, Niall A. Schulz-Trieglaff, Ole Smith, Geoffrey P. Evers, Dirk J. Pevzner, Pavel A. Lasken, Roger S. Nat Biotechnol Article Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of genomes from single cells of bacteria that cannot be cultured. However, genome assembly is challenging because of highly non-uniform read coverage generated by MDA. We describe an improved assembly approach tailored for single cell Illumina sequences that incorporates a progressively increasing coverage cutoff. This allows variable coverage datasets to be utilized effectively with assembly of E. coli and S. aureus single cell reads capturing >91% of genes within contigs, approaching the 95% captured from a multi-cell E. coli assembly. We apply this method to assemble a single cell genome of the uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. These new methods enable acquisition of genome assemblies for individual uncultivated bacteria, providing cell-specific genetic information absent from metagenomic studies. 2011-09-18 /pmc/articles/PMC3558281/ /pubmed/21926975 http://dx.doi.org/10.1038/nbt.1966 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Chitsaz, Hamidreza Yee-Greenbaum, Joyclyn L. Tesler, Glenn Lombardo, Mary-Jane Dupont, Christopher L. Badger, Jonathan H. Novotny, Mark Rusch, Douglas B. Fraser, Louise J. Gormley, Niall A. Schulz-Trieglaff, Ole Smith, Geoffrey P. Evers, Dirk J. Pevzner, Pavel A. Lasken, Roger S. De novo assembly of bacterial genomes from single cells |
title | De novo assembly of bacterial genomes from single cells |
title_full | De novo assembly of bacterial genomes from single cells |
title_fullStr | De novo assembly of bacterial genomes from single cells |
title_full_unstemmed | De novo assembly of bacterial genomes from single cells |
title_short | De novo assembly of bacterial genomes from single cells |
title_sort | de novo assembly of bacterial genomes from single cells |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558281/ https://www.ncbi.nlm.nih.gov/pubmed/21926975 http://dx.doi.org/10.1038/nbt.1966 |
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