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Updated: Jul 27, 2025
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
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Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes
Rohan S Mehta1, Robert A Petit2,3, Timothy D Read2,4
1Department of Physics, Emory University, Atlanta, GA, USA. rsmeht4@emory.edu.
BMC Bioinformatics
|June 9, 2023
Summary
Researchers developed a new method to detect coevolving genes in bacterial genomes by comparing closely related individuals. This approach reveals coordinated gene gain/loss events, highlighting networks of genes involved in virulence and antibiotic resistance in Staphylococcus aureus.
Area of Science:
- Genomics
- Microbial Evolution
- Bioinformatics
Background:
- Bacterial genomes are highly dynamic due to extensive horizontal gene transfer.
- Inferring genetic interactions is challenging due to variable genome content.
Purpose of the Study:
- To develop a novel computational method for detecting coevolving genes in bacterial populations.
- To identify networks of genes that are gained or lost in a coordinated manner.
Main Methods:
- A pairwise comparison approach using closely related bacterial genomes, analogous to eukaryotic pedigree studies.
- Application to the Staphylococcus aureus accessory genome using a large dataset of over 40,000 whole genomes.
- Identification of gene pairs exhibiting coordinated gain/loss or compensatory gain/loss.
Main Results:
- Discovery of numerous gene pairs with coordinated gain or loss events.
- Identification of networks of coevolving genes, particularly those related to virulence, horizontal gene transfer, and antibiotic resistance (e.g., SCCmec).
- Demonstration of the method's applicability to detecting co-substitution and genotype-phenotype coevolution.
Conclusions:
- The developed method effectively identifies coevolving gene networks in bacteria.
- Coevolutionary patterns are prominent in genes associated with key bacterial adaptations like virulence and antibiotic resistance.
- The R package DeCoTUR provides a computational tool for applying this method.
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