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Updated: May 22, 2026
06:56
Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
Published on: March 24, 2023
Genetic relationships among 527 Gram-negative bacterial plasmids
Yunyun Zhou1, Douglas R Call, Shira L Broschat
1School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA.
Plasmid
|May 17, 2012
Summary
We developed a novel computational method to analyze genetic relationships among 527 Gram-negative bacterial plasmids. This virtual hybridization approach accurately predicts plasmid relationships and aids in studying antibiotic resistance gene distribution.
Area of Science:
- Microbiology
- Bioinformatics
- Genetics
Background:
- Plasmids exhibit mosaic genetic structures due to horizontal gene transfer, complicating phylogenetic analysis.
- Understanding plasmid genetic relationships is crucial for microbial genetics and epidemiology.
Purpose of the Study:
- To develop and validate a computational method for analyzing genetic relationships among a large collection of Gram-negative bacterial plasmids.
- To apply this method to investigate the distribution of antibiotic resistance genes within plasmid populations.
Main Methods:
- Acquired complete coding gene sequences for 527 Gram-negative bacterial plasmids from NCBI.
- Employed a "virtual hybridization" approach using BLASTp with protein sequences as probes.
- Constructed phylogenetic trees from distance matrices and refined relationships using conserved proteins and maximum likelihood analysis.
Main Results:
- Generated a phylogenetic tree encompassing 527 Gram-negative bacterial plasmids.
- Validated the method's accuracy through replication with IncA/C plasmids and consistency with Borrelia plasmid clustering.
- Analyzed the distribution patterns of four common antibiotic resistance genes across the plasmid tree.
Conclusions:
- The "virtual hybridization" method provides a robust approach for deciphering complex plasmid genetic relationships.
- This methodology facilitates large-scale plasmid phylogenetic studies and the investigation of mobile genetic elements like antibiotic resistance genes.
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