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Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow
Published on: June 14, 2017
Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF
Thomas Schillinger1, Mohamed Lisfi, Jingyun Chi
1Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany.
BMC Genomics
|August 30, 2012
Summary
Diversity Generating Retroelements (DGRs) are genetic elements that enhance bacterial adaptation. A new tool, DiGReF, identified 155 DGRs across bacteria, revealing their mobility and flexible mechanisms.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Diversity Generating Retroelements (DGRs) are genetic elements conferring adaptive advantages by generating diversity in host genomes.
- Unlike selfish elements, DGRs enhance host survival through hypermutation of specific genomic regions.
- Initially found in bacteriophages, DGRs have since been identified in various bacterial genomes.
Purpose of the Study:
- To develop and utilize a computational tool for comprehensive identification of DGRs in genomic databases.
- To analyze the distribution, mobility, and molecular mechanisms of DGRs in bacteria.
Main Methods:
- Development of the DiGReF program for large-scale DGR screening.
- Phylogenetic analysis and sequence comparison of identified DGRs.
- Genomic data analysis to infer DGR molecular mechanisms.
Main Results:
- Identification of 155 DGRs distributed sporadically across major bacterial classes.
- Evidence of DGR horizontal transfer via mobile genetic elements (phages, transposons, plasmids).
- Demonstration of DGR component flexibility and acquisition of target genes.
- New insights into DGRs, suggesting separate transcription of template RNA.
Conclusions:
- DiGReF is an effective tool for DGR detection and analysis in genomic data.
- The study deepens understanding of DGRs' role in prokaryotic genome plasticity.
- Findings provide insights into DGRs from a global to molecular level.
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