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Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
Published on: January 22, 2018
Classification of plant associated bacteria using RIF, a computationally derived DNA marker
Kevin L Schneider1, Glorimar Marrero, Anne M Alvarez
1Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.
Plos One
|May 3, 2011
Summary
A new DNA marker from the dnaA replication initiation factor (RIF) effectively distinguishes plant-associated bacteria, including Xanthomonas species. This RIF marker offers higher success rates and improved bacterial classification below the species level compared to traditional methods.
Area of Science:
- Bacteriology
- Molecular Biology
- Plant Pathology
Background:
- Accurate identification of plant-associated bacteria is crucial for managing agricultural diseases.
- Existing methods using ribosomal genes can be less effective for differentiating closely related species.
- The genus Xanthomonas includes significant phytopathogens requiring precise taxonomic tools.
Purpose of the Study:
- To develop a novel DNA marker for bacterial identification at the species level and below.
- To evaluate the efficacy of the dnaA replication initiation factor (RIF) as a taxonomic marker.
- To create a database and frameworks for rapid bacterial classification and diagnostics.
Main Methods:
- Comparative genomic analysis of six Xanthomonas genomes to identify a suitable DNA marker.
- Development of genus-specific primers for amplifying the RIF marker.
- In silico and experimental sequencing of RIF from diverse bacterial strains (Xanthomonas, Ralstonia, Clavibacter, Enterobacteriaceae).
- Construction of RIF sequence frameworks and database (RIFdb).
Main Results:
- The RIF marker demonstrated equal or greater discriminatory power than the ribosomal intergenic spacer region (ITS) for Xanthomonas species.
- RIF sequencing achieved a 16% higher success rate compared to ITS in a large strain collection.
- RIF analysis revealed subspecific groupings but indicated that current pathovar and race designations may not reflect true genetic relationships.
- RIF frameworks successfully classified previously uncharacterized strains and matched them to known reference strains.
Conclusions:
- The dnaA replication initiation factor (RIF) is a robust and highly effective DNA marker for bacterial taxonomy.
- RIF provides superior resolution for differentiating closely related bacterial strains, including phytopathogens.
- The RIFdb database and frameworks offer a valuable tool for rapid bacterial diagnostics and classification below the species level.
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