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Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the...

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Autores principales: Schneider, Kevin L., Marrero, Glorimar, Alvarez, Anne M., Presting, Gernot G.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080875/
https://www.ncbi.nlm.nih.gov/pubmed/21533033
http://dx.doi.org/10.1371/journal.pone.0018496
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author Schneider, Kevin L.
Marrero, Glorimar
Alvarez, Anne M.
Presting, Gernot G.
author_facet Schneider, Kevin L.
Marrero, Glorimar
Alvarez, Anne M.
Presting, Gernot G.
author_sort Schneider, Kevin L.
collection PubMed
description A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format.
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spelling pubmed-30808752011-04-29 Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker Schneider, Kevin L. Marrero, Glorimar Alvarez, Anne M. Presting, Gernot G. PLoS One Research Article A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format. Public Library of Science 2011-04-21 /pmc/articles/PMC3080875/ /pubmed/21533033 http://dx.doi.org/10.1371/journal.pone.0018496 Text en Schneider et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Schneider, Kevin L.
Marrero, Glorimar
Alvarez, Anne M.
Presting, Gernot G.
Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title_full Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title_fullStr Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title_full_unstemmed Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title_short Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker
title_sort classification of plant associated bacteria using rif, a computationally derived dna marker
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080875/
https://www.ncbi.nlm.nih.gov/pubmed/21533033
http://dx.doi.org/10.1371/journal.pone.0018496
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