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Engineering and Analyzing Multicellular Systems

Volume 1151 of the series Methods in Molecular Biology pp 165-188

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Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq

  • Daniel E. DeatherageAffiliated withDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin
  • , Jeffrey E. BarrickAffiliated withDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin Email author 

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Abstract

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.

Key words

Evolutionary genomics Genome re-sequencing Variant caller Single-nucleotide variant Structural variant Insertion sequence Mobile genetic element Gene conversion