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      Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

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          Abstract

          Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.

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          Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.

          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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            Completing bacterial genome assemblies with multiplex MinION sequencing

            Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure. This has major implications for tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a bacterial genome requires long-read sequencing such as those generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use of the ONT MinION to sequence 12 isolates of Klebsiella pneumoniae on a single flow cell. We assembled each genome using a combination of ONT reads and previously available Illumina reads, and little to no manual intervention was needed to achieve fully resolved assemblies using the Unicycler hybrid assembler. Assembling only ONT reads with Canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with Nanopolish. We demonstrate that multiplexed ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Specifically, we advocate the use of Illumina sequencing as a first analysis step, followed by ONT reads as needed to resolve genomic structure.
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              Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations

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                Author and article information

                Contributors
                mike.mcdonald@monash.edu
                Journal
                EMBO Rep
                EMBO Rep
                10.1002/(ISSN)1469-3178
                EMBR
                embor
                EMBO Reports
                John Wiley and Sons Inc. (Hoboken )
                1469-221X
                1469-3178
                24 July 2019
                August 2019
                24 July 2019
                : 20
                : 8 ( doiID: 10.1002/embr.v20.8 )
                : e46992
                Affiliations
                [ 1 ] School of Biological Sciences Monash University Melbourne Vic. Australia
                Author notes
                [*] [* ]Corresponding author. Tel: +61 3 9905 1697; E‐mail: mike.mcdonald@ 123456monash.edu
                Author information
                https://orcid.org/0000-0002-5735-960X
                Article
                EMBR201846992
                10.15252/embr.201846992
                6680118
                31338963
                fc3f2ae3-1eeb-4e09-91ea-c7a6ae725a27
                © 2019 The Author. Published under the terms of the CC BY 4.0 license

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 01 September 2018
                : 23 March 2019
                : 28 June 2019
                Page count
                Figures: 3, Tables: 0, Pages: 14, Words: 12305
                Funding
                Funded by: Department of Education and Training|Australian Research Council (ARC)
                Award ID: FT170100441
                Award ID: DP180102161
                Categories
                Review
                Review
                Custom metadata
                2.0
                embr201846992
                August 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.7 mode:remove_FC converted:05.08.2019

                Molecular biology
                adaptation,directed evolution,experimental evolution,microbiome evolution,selection,evolution,microbiology, virology & host pathogen interaction

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