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Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

Leah H. Burdick, View ORCID ProfileJared C. Streich, View ORCID ProfileDelyana P. Vasileva, Dawn M. Klingeman, View ORCID ProfileHari B. Chhetri, View ORCID ProfileJ. Christopher Ellis, View ORCID ProfileDan M. Close, View ORCID ProfileDaniel A. Jacobson, View ORCID ProfileJoshua K. Michener
doi: https://doi.org/10.1101/2020.10.06.328625
Leah H. Burdick
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Jared C. Streich
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Delyana P. Vasileva
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Dawn M. Klingeman
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Hari B. Chhetri
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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J. Christopher Ellis
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Dan M. Close
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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  • ORCID record for Dan M. Close
Daniel A. Jacobson
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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  • For correspondence: jacobsonda@ornl.gov michenerjk@ornl.gov
Joshua K. Michener
1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
2Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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  • For correspondence: jacobsonda@ornl.gov michenerjk@ornl.gov
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ABSTRACT

In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Computational analyses suggested that this bias is due to the action of restriction-modification systems whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that the intensity of recombination is uniform across the genome without concentration into hotspots. Unexpectedly, our results revealed that large species-level genetic distance did not affect key recombination parameters. Our study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

Competing Interest Statement

JCS, DPV, DAJ, and JKM are inventors on a patent that has been filed based, in part, on the work reported in this manuscript.

Footnotes

  • Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination
Leah H. Burdick, Jared C. Streich, Delyana P. Vasileva, Dawn M. Klingeman, Hari B. Chhetri, J. Christopher Ellis, Dan M. Close, Daniel A. Jacobson, Joshua K. Michener
bioRxiv 2020.10.06.328625; doi: https://doi.org/10.1101/2020.10.06.328625
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Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination
Leah H. Burdick, Jared C. Streich, Delyana P. Vasileva, Dawn M. Klingeman, Hari B. Chhetri, J. Christopher Ellis, Dan M. Close, Daniel A. Jacobson, Joshua K. Michener
bioRxiv 2020.10.06.328625; doi: https://doi.org/10.1101/2020.10.06.328625

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