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 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.
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H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 |
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H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 Prior, Philippe Ailloud, Florent Dalsing, Beth Remenant, Benoit Sanchez, Borja Allen, Caitilyn Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species |
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. |
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article |
topic_facet |
H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Prior, Philippe Ailloud, Florent Dalsing, Beth Remenant, Benoit Sanchez, Borja Allen, Caitilyn |
author_facet |
Prior, Philippe Ailloud, Florent Dalsing, Beth Remenant, Benoit Sanchez, Borja Allen, Caitilyn |
author_sort |
Prior, Philippe |
title |
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_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_sort |
genomic and proteomic evidence supporting the division of the plant pathogen ralstonia solanacearum into three species |
url |
http://agritrop.cirad.fr/579916/ http://agritrop.cirad.fr/579916/1/579916.pdf |
work_keys_str_mv |
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1792499019172282368 |
spelling |
dig-cirad-fr-5799162024-01-28T23:22:27Z http://agritrop.cirad.fr/579916/ http://agritrop.cirad.fr/579916/ Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. Prior Philippe, Ailloud Florent, Dalsing Beth, Remenant Benoit, Sanchez Borja, Allen Caitilyn. 2016. BMC Genomics, 17 (1), 11 p.https://doi.org/10.1186/s12864-016-2413-z <https://doi.org/10.1186/s12864-016-2413-z> Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species Prior, Philippe Ailloud, Florent Dalsing, Beth Remenant, Benoit Sanchez, Borja Allen, Caitilyn eng 2016 BMC Genomics H20 - Maladies des plantes Ralstonia solanacearum espèce identification taxonomie génomique variation génétique génome pouvoir pathogène métabolisme de l'azote phylogénie flétrissement Ralstonia http://aims.fao.org/aos/agrovoc/c_37076 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_3791 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5629 http://aims.fao.org/aos/agrovoc/c_5197 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_37842 La Réunion France http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/579916/1/579916.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/s12864-016-2413-z 10.1186/s12864-016-2413-z info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-016-2413-z info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12864-016-2413-z |