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Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequili...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906370/ https://www.ncbi.nlm.nih.gov/pubmed/33630832 http://dx.doi.org/10.1371/journal.pone.0242297 |
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author | Louha, Swarnali Meinersmann, Richard J. Glenn, Travis C. |
author_facet | Louha, Swarnali Meinersmann, Richard J. Glenn, Travis C. |
author_sort | Louha, Swarnali |
collection | PubMed |
description | We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with ~99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential “hot spots” for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium in L. monocytogenes suggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures. |
format | Online Article Text |
id | pubmed-7906370 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-79063702021-03-03 Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates Louha, Swarnali Meinersmann, Richard J. Glenn, Travis C. PLoS One Research Article We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with ~99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential “hot spots” for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium in L. monocytogenes suggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures. Public Library of Science 2021-02-25 /pmc/articles/PMC7906370/ /pubmed/33630832 http://dx.doi.org/10.1371/journal.pone.0242297 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Louha, Swarnali Meinersmann, Richard J. Glenn, Travis C. Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title | Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title_full | Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title_fullStr | Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title_full_unstemmed | Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title_short | Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates |
title_sort | whole genome genetic variation and linkage disequilibrium in a diverse collection of listeria monocytogenes isolates |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906370/ https://www.ncbi.nlm.nih.gov/pubmed/33630832 http://dx.doi.org/10.1371/journal.pone.0242297 |
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