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Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq
Open accessAbstract
Summary Next-generation DNA sequencing (NGS) can be used to reconstruct eco-evolutionary population dynamics and to identify the genetic basis of adaptation in laboratory evolution experiments. Here, we describe how to run the open-source breseq computational pipeline to identify and annotate genetic differences found in whole-genome and whole-population NGS data from haploid microbes where a high-quality reference genome is available. These methods can also be used to analyze mutants isolated in genetic screens and to detect unintended mutations that may occur during strain construction and genome editing.
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Cites
Versatile and open software for comparing large genomes
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Cited by
Federici, S., Kredo-Russo, S., Valdés-Mas, R., Kviatcovsky, D., Weinstock, E., Matiuhin, Y., Silberberg, Y., Atarashi, K., Furuichi, M., Oka, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.07.003 · Cited by 542
Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation
Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., Gerber, G. K., Way, J. C., & Silver, P. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3879 · Cited by 426
Sugar Synthesis from CO2 in Escherichia coli
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Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis
Yu, T., Zhou, Y. J., Huang, M., Liu, Q., Pereira, R., David, F., & Nielsen, J. (2018) · Cell · doi:10.1016/j.cell.2018.07.013 · Cited by 341
Rapid evolution of silver nanoparticle resistance in Escherichia coli
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Metadata
- Authors
- Deatherage, D. E., & Barrick, J. E.
- Venue
- Methods in Molecular Biology
- Publisher
- Springer New York
- Published
- 2014
- Volume
- 1151
- Pages
- 165-188
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2290768068
- Cited by
- 1,609
- References
- 2
- FWCI
- 62.12
- Type
- book chapter
- Language
- en
- Open access
- green
- Licence
- www.springernature.com/gp/researchers/text-and-data-mining (tdm)
- www.springernature.com/gp/researchers/text-and-data-mining (vor)
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- Deatherage, D. E., & Barrick, J. E. (2014). Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq. Methods in Molecular Biology. https://doi.org/10.1007/978-1-4939-0554-6_12
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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.
