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Genetic variation and linkage disequilibrium in Bacillus anthracis
We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240990/ https://www.ncbi.nlm.nih.gov/pubmed/22355684 http://dx.doi.org/10.1038/srep00169 |
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author | Zwick, Michael E. Thomason, Maureen Kiley Chen, Peter E. Johnson, Henry R. Sozhamannan, Shanmuga Mateczun, Alfred Read, Timothy D. |
author_facet | Zwick, Michael E. Thomason, Maureen Kiley Chen, Peter E. Johnson, Henry R. Sozhamannan, Shanmuga Mateczun, Alfred Read, Timothy D. |
author_sort | Zwick, Michael E. |
collection | PubMed |
description | We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains. |
format | Online Article Text |
id | pubmed-3240990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-32409902011-12-22 Genetic variation and linkage disequilibrium in Bacillus anthracis Zwick, Michael E. Thomason, Maureen Kiley Chen, Peter E. Johnson, Henry R. Sozhamannan, Shanmuga Mateczun, Alfred Read, Timothy D. Sci Rep Article We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains. Nature Publishing Group 2011-11-24 /pmc/articles/PMC3240990/ /pubmed/22355684 http://dx.doi.org/10.1038/srep00169 Text en Copyright © 2011, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-sa/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareALike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ |
spellingShingle | Article Zwick, Michael E. Thomason, Maureen Kiley Chen, Peter E. Johnson, Henry R. Sozhamannan, Shanmuga Mateczun, Alfred Read, Timothy D. Genetic variation and linkage disequilibrium in Bacillus anthracis |
title | Genetic variation and linkage disequilibrium in Bacillus anthracis |
title_full | Genetic variation and linkage disequilibrium in Bacillus anthracis |
title_fullStr | Genetic variation and linkage disequilibrium in Bacillus anthracis |
title_full_unstemmed | Genetic variation and linkage disequilibrium in Bacillus anthracis |
title_short | Genetic variation and linkage disequilibrium in Bacillus anthracis |
title_sort | genetic variation and linkage disequilibrium in bacillus anthracis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240990/ https://www.ncbi.nlm.nih.gov/pubmed/22355684 http://dx.doi.org/10.1038/srep00169 |
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