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Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat
Published on: September 20, 2016
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Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
Daniel E Deatherage1, Jeffrey E Barrick
1Department 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, 1 University Station A5300, Austin, TX, 78712, USA.
Methods in Molecular Biology (Clifton, N.J.)
|May 20, 2014
Summary
Next-generation sequencing (NGS) aids in understanding evolution and adaptation. The breseq pipeline efficiently identifies genetic variations in microbial populations using whole-genome sequencing data.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genetics
Background:
- Next-generation sequencing (NGS) offers powerful tools for studying population dynamics and genetic adaptation.
- Laboratory evolution experiments are crucial for dissecting the genetic underpinnings of adaptation.
- Analyzing microbial populations requires robust computational methods for genetic variation detection.
Purpose of the Study:
- To provide a guide for utilizing the open-source breseq computational pipeline.
- To detail the application of breseq for analyzing whole-genome and whole-population NGS data in haploid microbes.
- To demonstrate breseq's utility in identifying genetic differences and annotating mutations.
Main Methods:
- Utilizing the breseq computational pipeline for analyzing NGS data.
- Applying breseq to whole-genome sequencing data from haploid microbial populations.
- Leveraging a high-quality reference genome for accurate variant identification and annotation.
Main Results:
- breseq effectively identifies and annotates genetic differences in microbial populations.
- The pipeline is suitable for analyzing data from laboratory evolution experiments.
- breseq can detect unintended mutations in engineered strains.
Conclusions:
- The breseq pipeline is a valuable tool for genetic analysis of microbial populations.
- This method facilitates the reconstruction of eco-evolutionary dynamics.
- breseq aids in understanding adaptation and validating genetic modifications.
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