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Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

BACKGROUND: The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these ge...

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Autores principales: Prior, Philippe, Ailloud, Florent, Dalsing, Beth L., Remenant, Benoit, Sanchez, Borja, Allen, Caitilyn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736150/
https://www.ncbi.nlm.nih.gov/pubmed/26830494
http://dx.doi.org/10.1186/s12864-016-2413-z
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author Prior, Philippe
Ailloud, Florent
Dalsing, Beth L.
Remenant, Benoit
Sanchez, Borja
Allen, Caitilyn
author_facet Prior, Philippe
Ailloud, Florent
Dalsing, Beth L.
Remenant, Benoit
Sanchez, Borja
Allen, Caitilyn
author_sort Prior, Philippe
collection PubMed
description BACKGROUND: The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants. RESULTS: We used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species. CONCLUSIONS: Together, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2413-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-47361502016-02-03 Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species Prior, Philippe Ailloud, Florent Dalsing, Beth L. Remenant, Benoit Sanchez, Borja Allen, Caitilyn BMC Genomics Research Article BACKGROUND: The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants. RESULTS: We used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species. CONCLUSIONS: Together, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2413-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-02-01 /pmc/articles/PMC4736150/ /pubmed/26830494 http://dx.doi.org/10.1186/s12864-016-2413-z Text en © Prior et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Prior, Philippe
Ailloud, Florent
Dalsing, Beth L.
Remenant, Benoit
Sanchez, Borja
Allen, Caitilyn
Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title_full Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title_fullStr Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title_full_unstemmed Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title_short Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species
title_sort genomic and proteomic evidence supporting the division of the plant pathogen ralstonia solanacearum into three species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736150/
https://www.ncbi.nlm.nih.gov/pubmed/26830494
http://dx.doi.org/10.1186/s12864-016-2413-z
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