Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)

Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic...

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Autores principales: Wang, Aisuo, Ash, Gavin J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555171/
http://dx.doi.org/10.1038/srep13644
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author Wang, Aisuo
Ash, Gavin J.
author_facet Wang, Aisuo
Ash, Gavin J.
author_sort Wang, Aisuo
collection PubMed
description Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).
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spelling pubmed-45551712015-09-11 Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP) Wang, Aisuo Ash, Gavin J. Sci Rep Article Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method). Nature Publishing Group 2015-09-01 /pmc/articles/PMC4555171/ http://dx.doi.org/10.1038/srep13644 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Wang, Aisuo
Ash, Gavin J.
Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title_full Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title_fullStr Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title_full_unstemmed Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title_short Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
title_sort whole genome phylogeny of bacillus by feature frequency profiles (ffp)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555171/
http://dx.doi.org/10.1038/srep13644
work_keys_str_mv AT wangaisuo wholegenomephylogenyofbacillusbyfeaturefrequencyprofilesffp
AT ashgavinj wholegenomephylogenyofbacillusbyfeaturefrequencyprofilesffp

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