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De novo assembly of bacterial genomes from single cells
| Content Provider | Semantic Scholar |
|---|---|
| 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 Paul Evers, Dirk J. Pevzner, Pavel A. Lasken, Roger S. |
| Copyright Year | 2011 |
| Abstract | 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 cellspecific genetic information absent from metagenomic studies. Users may view, print, copy, download and text and datamine 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 Corresponding author (rlasken@jcvi.org). 7These authors contributed equally to this work. Author contributions All authors analyzed data. H.C. and G.T. wrote software. M.N., J.Y.-G, M.-J.L., and L.J.F. performed wetlab experiments. H.C., J.Y.-G., G.T., C.L.D., M.-J.L., L.J.F., N.A.G., P.A.P., and R.S.L. wrote the manuscript. H.C., G.T., M.-J.L., C.L.D., J.H.B., D.B.R., and N.A.G. created figures and tables. R.S.L. and M.-J.L. supervised the JCVI group. P.A.P. and G.T. supervised the UCSD group. N.A.G. and D.J.E. supervised the Illumina group. G.P.S. initiated the Illumina-JCVI collaboration. Note: Supplementary information is available on the Nature Biotechnology website. HHS Public Access Author manuscript Nat Biotechnol. Author manuscript; available in PMC 2013 January 29. Published in final edited form as: Nat Biotechnol. ; 29(10): 915–921. doi:10.1038/nbt.1966. A uhor M anscript |
| Starting Page | 915 |
| Ending Page | 921 |
| Page Count | 7 |
| File Format | PDF HTM / HTML |
| PubMed reference number | 21926975 |
| Volume Number | 29 |
| Alternate Webpage(s) | http://www.ttaxus.com/files/chitsaz2011-assembly.pdf |
| Journal | Nature biotechnology |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
