The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
Open accessAbstract
BACKGROUND: Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA) and complete genome sequencing of individual cells. METHODOLOGY/PRINCIPAL FINDINGS: We describe a pipeline that enables single-cell WGA on hundreds of cells at a time while virtually eliminating non-target DNA from the reactions. We further developed a post-amplification normalization procedure that mitigates extreme variations in sequencing coverage associated with multiple displacement amplification (MDA), and demonstrated that the procedure increased sequencing efficiency and facilitated genome assembly. We report genome recovery as high as 99.6% with reference-guided assembly, and 95% with de novo assembly starting from a single cell. We also analyzed the impact of chimera formation during MDA on de novo assembly, and discuss strategies to minimize the presence of incorrectly joined regions in contigs. CONCLUSIONS/SIGNIFICANCE: The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.
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Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293
Cited by
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,987
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013) · Nature Biotechnology · doi:10.1038/nbt.2579 · Cited by 1,251
Manichanh, C., Borruel, N., Casellas, F., & Guarner, F. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.152 · Cited by 1,160
Droplet microfluidics for high-throughput biological assays
Guo, M. T., Rotem, A., Heyman, J. A., & Weitz, D. A. (2012) · Lab on a Chip · doi:10.1039/c2lc21147e · Cited by 1,040
The human microbiome: Our second genome
Grice, E. A., & Segre, J. A. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163814 · Cited by 759
Metadata
- Authors
- Rodrigue, S., Malmstrom, R. R., Berlin, A. M., Birren, B. W., Henn, M. R., & Chisholm, S. W.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-09-02
- Volume
- 4
- Issue
- 9
- Pages
- e6864
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2149770991
- Cited by
- 258
- References
- 3
- FWCI
- 9.12
- Type
- journal article
- Language
- en
- Open access
- gold
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- Rodrigue, S., Malmstrom, R. R., Berlin, A. M., Birren, B. W., Henn, M. R., & Chisholm, S. W. (2009). Whole Genome Amplification and De novo Assembly of Single Bacterial Cells. PLoS ONE. https://doi.org/10.1371/journal.pone.0006864
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
